Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon
Andressa Monteiro Venturini
Generated January 6, 2025

Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon

Andressa M. Venturini

Genome-resolved metagenomics was applied to recover soil archaeal and bacterial metagenome-assembled genomes (MAGs) from three forests and three pastures of the Brazilian Eastern Amazon during dry and rainy seasons.

Table of Contents

  • Brief sample description
  • 1. Data importing
  • 2. Data trimming and filtering
  • 3. Read merging
  • 4. Read assembly
  • 5. Contig binning
  • 6. MAG quality filtering
  • 7. MAG extraction and quality assessment
  • 8. Taxonomic classification
  • 9. ANI comparisons
  • 10. Functional annotation
  • 11. Coverage calculation for high-quality MAGs

    • Brief sample description

    ID Season Land use Site Point
    C1 Dry Forest FP2 1
    C2 Dry Forest FP2 3
    C3 Dry Forest FP2 5
    C4 Dry Forest FP4 1
    C5 Dry Forest FP4 3
    C6 Dry Forest FP4 5
    C7 Dry Forest FP5 1
    C8 Dry Forest FP5 3
    C9 Dry Forest FP5 5
    C10 Dry Pasture P2 1
    C11 Dry Pasture P2 3
    C12 Dry Pasture P2 5
    C13 Dry Pasture P3 1
    C14 Dry Pasture P3 3
    C15 Dry Pasture P3 5
    C16 Dry Pasture P4 1
    C17 Dry Pasture P4 3
    C18 Dry Pasture P4 5
    C19 Rainy Forest FP2 1
    C20 Rainy Forest FP2 3
    C21 Rainy Forest FP2 5
    C22 Rainy Forest FP4 1
    C23 Rainy Forest FP4 3
    C24 Rainy Forest FP4 5
    C25 Rainy Forest FP5 1
    C26 Rainy Forest FP5 3
    C27 Rainy Forest FP5 5
    C28 Rainy Pasture P2 1
    C29 Rainy Pasture P2 3
    C30 Rainy Pasture P2 5
    C31 Rainy Pasture P3 1
    C32 Rainy Pasture P3 3
    C33 Rainy Pasture P3 5
    C34 Rainy Pasture P4 1
    C35 Rainy Pasture P4 3
    C36 Rainy Pasture P4 5

    1. Data importing

    from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "fastq_fwd_staging_file_name": "A1_1.fq.gz",
            "fastq_rev_staging_file_name": "A1_2.fq.gz",
            "name": "C1"
        }, {
            "fastq_fwd_staging_file_name": "A2_1.fq.gz",
            "fastq_rev_staging_file_name": "A2_2.fq.gz",
            "name": "C2"
        }, {
            "fastq_fwd_staging_file_name": "A3_1.fq.gz",
            "fastq_rev_staging_file_name": "A3_2.fq.gz",
            "name": "C3"
        }, {
            "fastq_fwd_staging_file_name": "A4_1.fq.gz",
            "fastq_rev_staging_file_name": "A4_2.fq.gz",
            "name": "C4"
        }, {
            "fastq_fwd_staging_file_name": "A5_1.fq.gz",
            "fastq_rev_staging_file_name": "A5_2.fq.gz",
            "name": "C5"
        }, {
            "fastq_fwd_staging_file_name": "A6_1.fq.gz",
            "fastq_rev_staging_file_name": "A6_2.fq.gz",
            "name": "C6"
        }, {
            "fastq_fwd_staging_file_name": "A7_1.fq.gz",
            "fastq_rev_staging_file_name": "A7_2.fq.gz",
            "name": "C7"
        }, {
            "fastq_fwd_staging_file_name": "A8_1.fq.gz",
            "fastq_rev_staging_file_name": "A8_2.fq.gz",
            "name": "C8"
        }, {
            "fastq_fwd_staging_file_name": "A9_1.fq.gz",
            "fastq_rev_staging_file_name": "A9_2.fq.gz",
            "name": "C9"
        }, {
            "fastq_fwd_staging_file_name": "A10_1.fq.gz",
            "fastq_rev_staging_file_name": "A10_2.fq.gz",
            "name": "C10"
        }],
        "shared_params": {
            "sequencing_tech": "Illumina",
            "single_genome": 0,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }
    }],
    cell_id="cf086e35-8792-41e4-b09c-833a9a946387",
    run_id="25ef01af-aae9-4967-bc08-86d7916f8444"
)

    from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "fastq_fwd_staging_file_name": "A11_1.fq.gz",
            "fastq_rev_staging_file_name": "A11_2.fq.gz",
            "name": "C11"
        }, {
            "fastq_fwd_staging_file_name": "A12_1.fq.gz",
            "fastq_rev_staging_file_name": "A12_2.fq.gz",
            "name": "C12"
        }, {
            "fastq_fwd_staging_file_name": "A13_1.fq.gz",
            "fastq_rev_staging_file_name": "A13_2.fq.gz",
            "name": "C13"
        }, {
            "fastq_fwd_staging_file_name": "A14_1.fq.gz",
            "fastq_rev_staging_file_name": "A14_2.fq.gz",
            "name": "C14"
        }, {
            "fastq_fwd_staging_file_name": "A15_1.fq.gz",
            "fastq_rev_staging_file_name": "A15_2.fq.gz",
            "name": "C15"
        }, {
            "fastq_fwd_staging_file_name": "A16_1.fq.gz",
            "fastq_rev_staging_file_name": "A16_2.fq.gz",
            "name": "C16"
        }, {
            "fastq_fwd_staging_file_name": "A17_1.fq.gz",
            "fastq_rev_staging_file_name": "A17_2.fq.gz",
            "name": "C17"
        }, {
            "fastq_fwd_staging_file_name": "A18_1.fq.gz",
            "fastq_rev_staging_file_name": "A18_2.fq.gz",
            "name": "C18"
        }, {
            "fastq_fwd_staging_file_name": "A19_1.fq.gz",
            "fastq_rev_staging_file_name": "A19_2.fq.gz",
            "name": "C19"
        }, {
            "fastq_fwd_staging_file_name": "A20_1.fq.gz",
            "fastq_rev_staging_file_name": "A20_2.fq.gz",
            "name": "C20"
        }],
        "shared_params": {
            "sequencing_tech": "Illumina",
            "single_genome": 0,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }
    }],
    cell_id="f779e14c-ab95-4d0a-8c67-900fd328f639",
    run_id="973059c3-f254-4147-982e-b6a578fc83d4"
)

    from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "fastq_fwd_staging_file_name": "A21_1.fq.gz",
            "fastq_rev_staging_file_name": "A21_2.fq.gz",
            "name": "C21"
        }, {
            "fastq_fwd_staging_file_name": "A22_1.fq.gz",
            "fastq_rev_staging_file_name": "A22_2.fq.gz",
            "name": "C22"
        }, {
            "fastq_fwd_staging_file_name": "A23_1.fq.gz",
            "fastq_rev_staging_file_name": "A23_2.fq.gz",
            "name": "C23"
        }, {
            "fastq_fwd_staging_file_name": "A24_1.fq.gz",
            "fastq_rev_staging_file_name": "A24_2.fq.gz",
            "name": "C24"
        }, {
            "fastq_fwd_staging_file_name": "A25_1.fq.gz",
            "fastq_rev_staging_file_name": "A25_2.fq.gz",
            "name": "C25"
        }, {
            "fastq_fwd_staging_file_name": "A26_1.fq.gz",
            "fastq_rev_staging_file_name": "A26_2.fq.gz",
            "name": "C26"
        }, {
            "fastq_fwd_staging_file_name": "A27_1.fq.gz",
            "fastq_rev_staging_file_name": "A27_2.fq.gz",
            "name": "C27"
        }, {
            "fastq_fwd_staging_file_name": "A28_1.fq.gz",
            "fastq_rev_staging_file_name": "A28_2.fq.gz",
            "name": "C28"
        }, {
            "fastq_fwd_staging_file_name": "A29_1.fq.gz",
            "fastq_rev_staging_file_name": "A29_2.fq.gz",
            "name": "C29"
        }, {
            "fastq_fwd_staging_file_name": "A30_1.fq.gz",
            "fastq_rev_staging_file_name": "A30_2.fq.gz",
            "name": "C30"
        }],
        "shared_params": {
            "sequencing_tech": "Illumina",
            "single_genome": 0,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }
    }],
    cell_id="b67d7816-4ce0-4b8d-b68e-a52e78dcbbd6",
    run_id="45564e56-2ed3-455c-9765-082eb2af67d8"
)

    from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "fastq_fwd_staging_file_name": "A31_1.fq.gz",
            "fastq_rev_staging_file_name": "A31_2.fq.gz",
            "name": "C31"
        }, {
            "fastq_fwd_staging_file_name": "A32_1.fq.gz",
            "fastq_rev_staging_file_name": "A32_2.fq.gz",
            "name": "C32"
        }, {
            "fastq_fwd_staging_file_name": "A33_1.fq.gz",
            "fastq_rev_staging_file_name": "A33_2.fq.gz",
            "name": "C33"
        }, {
            "fastq_fwd_staging_file_name": "A34_1.fq.gz",
            "fastq_rev_staging_file_name": "A34_2.fq.gz",
            "name": "C34"
        }, {
            "fastq_fwd_staging_file_name": "A35_1.fq.gz",
            "fastq_rev_staging_file_name": "A35_2.fq.gz",
            "name": "C35"
        }, {
            "fastq_fwd_staging_file_name": "A36_1.fq.gz",
            "fastq_rev_staging_file_name": "A36_2.fq.gz",
            "name": "C36"
        }],
        "shared_params": {
            "sequencing_tech": "Illumina",
            "single_genome": 0,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }
    }],
    cell_id="bcbe85ab-9f0c-42b7-a1e1-cec2c87de685",
    run_id="d0cdb0ef-a2db-43bb-a18e-aee80e4ef68e"
)

    2. Data trimming and filtering

    Obs.: The FastQC reports are in a private narrative but can be replicated by copying this narrative and re-running the apps.

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    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C22_127836_50_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C22_127836_50_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 24m 36s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C23_127836_59_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C23_127836_59_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 43s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C24_127836_51_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C24_127836_51_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 35s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C25_127836_49_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C25_127836_49_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 30s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C26_127836_60_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C26_127836_60_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 23m 54s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C27_127836_65_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C27_127836_65_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 46s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C28_127836_57_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C28_127836_57_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 23m 14s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C29_127836_63_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C29_127836_63_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 26m 1s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C30_127836_78_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C30_127836_78_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 25m 9s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C31_127836_67_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C31_127836_67_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 24m 50s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C32_127836_68_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C32_127836_68_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 23m 43s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C33_127836_70_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C33_127836_70_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 19m 44s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C34_127836_69_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C34_127836_69_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 23m 57s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C35_127836_75_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C35_127836_75_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 23m 59s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C36_127836_77_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C36_127836_77_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Build ReadsSet - v1.7.6
    Allows users to create a ReadsSet object.
    This app completed without errors in 35s.
    Objects
    Created Object Name Type Description
    Field_total ReadsSet KButil_Build_ReadsSet
    Summary
    reads libs in output set Field_total: 36
    Field_total
    v1 - KBaseSets.ReadsSet-1.2
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Trim Reads with Trimmomatic - v0.36
    Trim paired- or single-end Illumina reads with Trimmomatic.
    This app completed without errors in 1d 8h 50m 36s.
    Objects
    Created Object Name Type Description
    Field_total_cleaned_trimm_paired ReadsSet Trimmed Reads
    Field_total_cleaned_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
    Field_total_cleaned_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
    Field_total_cleaned_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
    Field_total_cleaned_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
    Field_total_cleaned_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
    Report
    Links
    Field_total_cleaned_trimm_paired_SampleSet
    v1 - KBaseRNASeq.RNASeqSampleSet-2.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Field_total_cleaned_trimm_paired
    v1 - KBaseSets.ReadsSet-1.2
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 11s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C1_trimm_paired_127836_371_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C1_trimm_paired_127836_371_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 19m 59s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C2_trimm_paired_127836_386_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C2_trimm_paired_127836_386_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 16s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C3_trimm_paired_127836_398_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C3_trimm_paired_127836_398_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 42s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C4_trimm_paired_127836_410_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C4_trimm_paired_127836_410_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 19m 35s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C5_trimm_paired_127836_422_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C5_trimm_paired_127836_422_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 14s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C6_trimm_paired_127836_434_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C6_trimm_paired_127836_434_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 49s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C7_trimm_paired_127836_443_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C7_trimm_paired_127836_443_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 17m 34s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C8_trimm_paired_127836_467_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C8_trimm_paired_127836_467_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 11m 9s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C9_trimm_paired_127836_477_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C9_trimm_paired_127836_477_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 11m 39s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C10_trimm_paired_127836_480_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C10_trimm_paired_127836_480_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 11m 56s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C11_trimm_paired_127836_486_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C11_trimm_paired_127836_486_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 15m 58s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C12_trimm_paired_127836_492_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C12_trimm_paired_127836_492_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 12m 53s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C13_trimm_paired_127836_505_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C13_trimm_paired_127836_505_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 12m 56s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C14_trimm_paired_127836_508_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C14_trimm_paired_127836_508_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 17m 57s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C15_trimm_paired_127836_511_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C15_trimm_paired_127836_511_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 17m 59s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C16_trimm_paired_127836_515_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C16_trimm_paired_127836_515_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 19m 32s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C17_trimm_paired_127836_529_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C17_trimm_paired_127836_529_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 17m 23s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C18_trimm_paired_127836_532_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C18_trimm_paired_127836_532_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 17m 19s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C19_trimm_paired_127836_535_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C19_trimm_paired_127836_535_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 19m 40s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C20_trimm_paired_127836_539_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C20_trimm_paired_127836_539_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 18m 54s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C21_trimm_paired_127836_542_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C21_trimm_paired_127836_542_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 19m 39s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C22_trimm_paired_127836_545_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C22_trimm_paired_127836_545_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 13m 5s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C23_trimm_paired_127836_549_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C23_trimm_paired_127836_549_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 13m 22s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C24_trimm_paired_127836_552_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C24_trimm_paired_127836_552_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 12m 50s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C25_trimm_paired_127836_555_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C25_trimm_paired_127836_555_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 12m 16s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C26_trimm_paired_127836_558_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C26_trimm_paired_127836_558_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 16m 9s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C27_trimm_paired_127836_561_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C27_trimm_paired_127836_561_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 13m 10s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C28_trimm_paired_127836_564_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C28_trimm_paired_127836_564_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 13m 36s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C29_trimm_paired_127836_567_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C29_trimm_paired_127836_567_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 16m 45s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C30_trimm_paired_127836_570_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C30_trimm_paired_127836_570_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 16m 51s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C31_trimm_paired_127836_573_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C31_trimm_paired_127836_573_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 17m 19s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C32_trimm_paired_127836_576_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C32_trimm_paired_127836_576_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 16m 44s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C33_trimm_paired_127836_579_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C33_trimm_paired_127836_579_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 13m 6s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C34_trimm_paired_127836_582_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C34_trimm_paired_127836_582_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 16m 22s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C35_trimm_paired_127836_585_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C35_trimm_paired_127836_585_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    Assess Read Quality with FastQC - v0.11.9
    A quality control application for high throughput sequence data.
    This app completed without errors in 16m 40s.
    Report
    Links
    • index.html - HTML files generated by fastqc that contains report on quality of reads
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • C36_trimm_paired_127836_588_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
    • C36_trimm_paired_127836_588_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report

    3. Read merging

    Merge Reads Libraries - v1.0.1
    Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
    This app completed without errors in 3h 5m 1s.
    Objects
    Created Object Name Type Description
    Field_forest_FP2_merged PairedEndLibrary Field samples - Forest - FP2 - From C1 to C3 and from C19 to C21.
    Summary
    NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
    Merge Reads Libraries - v1.0.1
    Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
    This app completed without errors in 2h 54m 34s.
    Objects
    Created Object Name Type Description
    Field_forest_FP4_merged PairedEndLibrary Field samples - Forest - FP4 - From C4 to C6 and from C22 to C24.
    Summary
    NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
    Merge Reads Libraries - v1.0.1
    Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
    This app completed without errors in 2h 29m 7s.
    Objects
    Created Object Name Type Description
    Field_forest_FP5_merged PairedEndLibrary Field samples - Forest - FP5 - From C7 to C9 and from C25 to C27.
    Summary
    NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
    Field_forest_FP2_merged
    v1 - KBaseFile.PairedEndLibrary-2.1
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Field_forest_FP4_merged
    v1 - KBaseFile.PairedEndLibrary-2.1
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Field_forest_FP5_merged
    v1 - KBaseFile.PairedEndLibrary-2.1
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Merge Reads Libraries - v1.0.1
    Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
    This app completed without errors in 2h 25m 2s.
    Objects
    Created Object Name Type Description
    Field_pasture_P2_merged PairedEndLibrary Field samples - Pasture - P2 - From C10 to C12 and from C28 to C30.
    Summary
    NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
    Merge Reads Libraries - v1.0.1
    Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
    This app completed without errors in 2h 36m 45s.
    Objects
    Created Object Name Type Description
    Field_pasture_P3_merged PairedEndLibrary Field samples - Pasture - P3 - From C13 to C15 and from C31 to C33.
    Summary
    NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
    Merge Reads Libraries - v1.0.1
    Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
    This app completed without errors in 2h 57m 12s.
    Objects
    Created Object Name Type Description
    Field_pasture_P4_merged PairedEndLibrary Field samples - Pasture - P4 - From C16 to C18 and from C34 to C36.
    Summary
    NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
    Field_pasture_P2_merged
    v1 - KBaseFile.PairedEndLibrary-2.1
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Field_pasture_P3_merged
    v1 - KBaseFile.PairedEndLibrary-2.1
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Field_pasture_P4_merged
    v1 - KBaseFile.PairedEndLibrary-2.1
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671

    4. Read assembly

    Assemble Reads with MEGAHIT v1.2.9
    Assemble metagenomic reads using the MEGAHIT assembler.
    This app completed without errors in 2d 13h 25m 19s.
    Objects
    Created Object Name Type Description
    Field_forest_FP2_MEGAHIT Assembly Assembled contigs
    Report
    Summary
    ContigSet saved to: andressamv:narrative_1664988165947/Field_forest_FP2_MEGAHIT Assembled into 322116 contigs. Avg Length: 3578.342836121149 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 321519 -- 2000.0 to 29060.2 bp 481 -- 29060.2 to 56120.4 bp 70 -- 56120.4 to 83180.6 bp 28 -- 83180.6 to 110240.8 bp 8 -- 110240.8 to 137301.0 bp 2 -- 137301.0 to 164361.2 bp 3 -- 164361.2 to 191421.4 bp 1 -- 191421.4 to 218481.6 bp 1 -- 218481.6 to 245541.80000000002 bp 3 -- 245541.80000000002 to 272602.0 bp
    Links
    Assemble Reads with MEGAHIT v1.2.9
    Assemble metagenomic reads using the MEGAHIT assembler.
    This app completed without errors in 2d 11h 50m 45s.
    Objects
    Created Object Name Type Description
    Field_forest_FP4_MEGAHIT Assembly Assembled contigs
    Report
    Summary
    ContigSet saved to: andressamv:narrative_1664988165947/Field_forest_FP4_MEGAHIT Assembled into 328152 contigs. Avg Length: 3531.281963846023 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 324564 -- 2000.0 to 13858.9 bp 3059 -- 13858.9 to 25717.8 bp 395 -- 25717.8 to 37576.7 bp 87 -- 37576.7 to 49435.6 bp 27 -- 49435.6 to 61294.5 bp 12 -- 61294.5 to 73153.4 bp 4 -- 73153.4 to 85012.3 bp 1 -- 85012.3 to 96871.2 bp 0 -- 96871.2 to 108730.09999999999 bp 3 -- 108730.09999999999 to 120589.0 bp
    Links
    Assemble Reads with MEGAHIT v1.2.9
    Assemble metagenomic reads using the MEGAHIT assembler.
    This app completed without errors in 2d 1h 53m 5s.
    Objects
    Created Object Name Type Description
    Field_forest_FP5_MEGAHIT Assembly Assembled contigs
    Report
    Summary
    ContigSet saved to: andressamv:narrative_1664988165947/Field_forest_FP5_MEGAHIT Assembled into 218238 contigs. Avg Length: 3414.8890294082607 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 216918 -- 2000.0 to 16327.7 bp 1093 -- 16327.7 to 30655.4 bp 170 -- 30655.4 to 44983.100000000006 bp 42 -- 44983.100000000006 to 59310.8 bp 8 -- 59310.8 to 73638.5 bp 5 -- 73638.5 to 87966.20000000001 bp 1 -- 87966.20000000001 to 102293.90000000001 bp 0 -- 102293.90000000001 to 116621.6 bp 0 -- 116621.6 to 130949.3 bp 1 -- 130949.3 to 145277.0 bp
    Links
    Assemble Reads with MEGAHIT v1.2.9
    Assemble metagenomic reads using the MEGAHIT assembler.
    This app completed without errors in 1d 21h 13m 59s.
    Objects
    Created Object Name Type Description
    Field_pasture_P2_MEGAHIT Assembly Assembled contigs
    Report
    Summary
    ContigSet saved to: andressamv:narrative_1664988165947/Field_pasture_P2_MEGAHIT Assembled into 239413 contigs. Avg Length: 3995.448388349839 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 238343 -- 2000.0 to 28088.5 bp 888 -- 28088.5 to 54177.0 bp 138 -- 54177.0 to 80265.5 bp 23 -- 80265.5 to 106354.0 bp 12 -- 106354.0 to 132442.5 bp 4 -- 132442.5 to 158531.0 bp 3 -- 158531.0 to 184619.5 bp 1 -- 184619.5 to 210708.0 bp 0 -- 210708.0 to 236796.5 bp 1 -- 236796.5 to 262885.0 bp
    Links
    Assemble Reads with MEGAHIT v1.2.9
    Assemble metagenomic reads using the MEGAHIT assembler.
    This app completed without errors in 2d 4h 10m 44s.
    Objects
    Created Object Name Type Description
    Field_pasture_P3_MEGAHIT Assembly Assembled contigs
    Report
    Summary
    ContigSet saved to: andressamv:narrative_1664988165947/Field_pasture_P3_MEGAHIT Assembled into 239213 contigs. Avg Length: 4163.110219762304 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 237370 -- 2000.0 to 27602.4 bp 1419 -- 27602.4 to 53204.8 bp 267 -- 53204.8 to 78807.20000000001 bp 91 -- 78807.20000000001 to 104409.6 bp 40 -- 104409.6 to 130012.0 bp 11 -- 130012.0 to 155614.40000000002 bp 7 -- 155614.40000000002 to 181216.80000000002 bp 6 -- 181216.80000000002 to 206819.2 bp 1 -- 206819.2 to 232421.6 bp 1 -- 232421.6 to 258024.0 bp
    Links
    Assemble Reads with MEGAHIT v1.2.9
    Assemble metagenomic reads using the MEGAHIT assembler.
    This app completed without errors in 2d 6h 16m 9s.
    Objects
    Created Object Name Type Description
    Field_pasture_P4_MEGAHIT Assembly Assembled contigs
    Report
    Summary
    ContigSet saved to: andressamv:narrative_1664988165947/Field_pasture_P4_MEGAHIT Assembled into 286013 contigs. Avg Length: 3925.7627450500504 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 283993 -- 2000.0 to 25082.9 bp 1515 -- 25082.9 to 48165.8 bp 323 -- 48165.8 to 71248.70000000001 bp 116 -- 71248.70000000001 to 94331.6 bp 37 -- 94331.6 to 117414.5 bp 13 -- 117414.5 to 140497.40000000002 bp 11 -- 140497.40000000002 to 163580.30000000002 bp 4 -- 163580.30000000002 to 186663.2 bp 0 -- 186663.2 to 209746.1 bp 1 -- 209746.1 to 232829.0 bp
    Links
    Assess Quality of Assemblies with QUAST - v4.4
    Run QUAST (QUality ASsessment Tool) on a set of Assemblies to assess their quality.
    This app completed without errors in 11m 16s.
    Report
    Summary
    All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). Assembly Field_forest_FP2_MEGAHIT Field_forest_FP4_MEGAHIT Field_forest_FP5_MEGAHIT Field_pasture_P2_MEGAHIT Field_pasture_P3_MEGAHIT Field_pasture_P4_MEGAHIT # contigs (>= 0 bp) 322116 328152 218238 239413 239213 286013 # contigs (>= 1000 bp) 322116 328152 218238 239413 239213 286013 # contigs (>= 10000 bp) 8562 8437 4604 11082 12032 11511 # contigs (>= 100000 bp) 23 3 1 25 74 52 # contigs (>= 1000000 bp) 0 0 0 0 0 0 Total length (>= 0 bp) 1152641481 1158797239 745258552 956562285 995870085 1122819180 Total length (>= 1000 bp) 1152641481 1158797239 745258552 956562285 995870085 1122819180 Total length (>= 10000 bp) 142420285 128950984 72452710 195134926 238114227 222866033 Total length (>= 100000 bp) 3565935 345379 145277 3331162 9810239 6709104 Total length (>= 1000000 bp) 0 0 0 0 0 0 # contigs 322116 328152 218238 239413 239213 286013 Largest contig 272602 120589 145277 262885 258024 232829 Total length 1152641481 1158797239 745258552 956562285 995870085 1122819180 GC (%) 63.13 63.25 61.87 66.59 67.24 65.93 N50 3478 3439 3283 4030 4234 3876 N75 2522 2511 2462 2660 2705 2621 L50 94136 97902 67338 59944 55398 72219 L75 192835 197917 133731 134605 130860 162161 # N's per 100 kbp 0.00 0.00 0.00 0.00 0.00 0.00
    Links

    5. Contig binning

    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 16h 28m 20s.
    Objects
    Created Object Name Type Description
    Field_forest_FP2_MaxBin2_107set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 17h 26m 36s.
    Objects
    Created Object Name Type Description
    Field_forest_FP2_MaxBin2_40set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 16h 28m 43s.
    Objects
    Created Object Name Type Description
    Field_forest_FP4_MaxBin2_107set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 17h 26m 54s.
    Objects
    Created Object Name Type Description
    Field_forest_FP4_MaxBin2_40set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 8h 34m 55s.
    Objects
    Created Object Name Type Description
    Field_forest_FP5_MaxBin2_107set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 9h 5m 17s.
    Objects
    Created Object Name Type Description
    Field_forest_FP5_MaxBin2_40set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 12h 7m 55s.
    Objects
    Created Object Name Type Description
    Field_pasture_P2_MaxBin2_107set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 13h 0m 10s.
    Objects
    Created Object Name Type Description
    Field_pasture_P2_MaxBin2_40set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 12h 52m 34s.
    Objects
    Created Object Name Type Description
    Field_pasture_P3_MaxBin2_107set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 13h 38m 12s.
    Objects
    Created Object Name Type Description
    Field_pasture_P3_MaxBin2_40set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 14h 53m 2s.
    Objects
    Created Object Name Type Description
    Field_pasture_P4_MaxBin2_107set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using MaxBin2 - v2.2.4
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
    This app completed without errors in 15h 43m 3s.
    Objects
    Created Object Name Type Description
    Field_pasture_P4_MaxBin2_40set BinnedContigs BinnedContigs from MaxBin2
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • maxbin_result.zip - File(s) generated by MaxBin2 App
    • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
    Output from Bin Contigs using MaxBin2 - v2.2.4
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    MetaBAT2 Contig Binning - v1.7
    Bin metagenomic contigs
    This app completed without errors in 6h 39m 26s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • metabat_result.zip - Files generated by MetaBAT2 App
    Output from MetaBAT2 Contig Binning - v1.7
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    MetaBAT2 Contig Binning - v1.7
    Bin metagenomic contigs
    This app completed without errors in 6h 43m 41s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • metabat_result.zip - Files generated by MetaBAT2 App
    Output from MetaBAT2 Contig Binning - v1.7
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    MetaBAT2 Contig Binning - v1.7
    Bin metagenomic contigs
    This app completed without errors in 4h 0m 48s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • metabat_result.zip - Files generated by MetaBAT2 App
    Output from MetaBAT2 Contig Binning - v1.7
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    MetaBAT2 Contig Binning - v1.7
    Bin metagenomic contigs
    This app completed without errors in 4h 51m 29s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • metabat_result.zip - Files generated by MetaBAT2 App
    Output from MetaBAT2 Contig Binning - v1.7
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    MetaBAT2 Contig Binning - v1.7
    Bin metagenomic contigs
    This app completed without errors in 4h 57m 46s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • metabat_result.zip - Files generated by MetaBAT2 App
    Output from MetaBAT2 Contig Binning - v1.7
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    MetaBAT2 Contig Binning - v1.7
    Bin metagenomic contigs
    This app completed without errors in 5h 58m 42s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • metabat_result.zip - Files generated by MetaBAT2 App
    Output from MetaBAT2 Contig Binning - v1.7
    The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Bin Contigs using CONCOCT - v1.1
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
    This app completed without errors in 6h 30m 9s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • concoct_result.zip - Files generated by CONCOCT App
    Bin Contigs using CONCOCT - v1.1
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
    This app completed without errors in 5h 50m 34s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • concoct_result.zip - Files generated by CONCOCT App
    Bin Contigs using CONCOCT - v1.1
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
    This app completed without errors in 4h 18m 58s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • concoct_result.zip - Files generated by CONCOCT App
    Bin Contigs using CONCOCT - v1.1
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
    This app completed without errors in 4h 13m 9s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • concoct_result.zip - Files generated by CONCOCT App
    Bin Contigs using CONCOCT - v1.1
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
    This app completed without errors in 4h 25m 51s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • concoct_result.zip - Files generated by CONCOCT App
    Bin Contigs using CONCOCT - v1.1
    Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
    This app completed without errors in 5h 4m 28s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • concoct_result.zip - Files generated by CONCOCT App
    Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
    This app completed without errors in 53m 5s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • das_tool_result.zip - Files generated by kb_das_tool App
    Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
    This app completed without errors in 52m 49s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • das_tool_result.zip - Files generated by kb_das_tool App
    Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
    This app completed without errors in 37m 6s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • das_tool_result.zip - Files generated by kb_das_tool App
    Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
    This app completed without errors in 37m 11s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • das_tool_result.zip - Files generated by kb_das_tool App
    Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
    This app completed without errors in 35m 28s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • das_tool_result.zip - Files generated by kb_das_tool App
    Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
    This app completed without errors in 41m 9s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • das_tool_result.zip - Files generated by kb_das_tool App

    6. MAG quality filtering

    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 26m 33s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 24m 48s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 13m 55s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 32m 56s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 27m 39s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 18m 48s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Filter Bins by Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
    This app completed without errors in 27m 33s.
    Objects
    Created Object Name Type Description
    Field_forest_FP2_CheckM_bins.BinnedContigs BinnedContigs HQ BinnedContigs Field_forest_FP2_CheckM_bins.BinnedContigs
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Field_forest_FP2_CheckM_bins.BinnedContigs
    v1 - KBaseMetagenomes.BinnedContigs-1.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Filter Bins by Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
    This app completed without errors in 25m 45s.
    Objects
    Created Object Name Type Description
    Field_forest_FP4_CheckM_bins.BinnedContigs BinnedContigs HQ BinnedContigs Field_forest_FP4_CheckM_bins.BinnedContigs
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Field_forest_FP4_CheckM_bins.BinnedContigs
    v1 - KBaseMetagenomes.BinnedContigs-1.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Filter Bins by Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
    This app completed without errors in 13m 53s.
    Objects
    Created Object Name Type Description
    Field_forest_FP5_CheckM_bins.BinnedContigs BinnedContigs HQ BinnedContigs Field_forest_FP5_CheckM_bins.BinnedContigs
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Field_forest_FP5_CheckM_bins.BinnedContigs
    v1 - KBaseMetagenomes.BinnedContigs-1.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Filter Bins by Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
    This app completed without errors in 33m 0s.
    Objects
    Created Object Name Type Description
    Field_pasture_P2_CheckM_bins.BinnedContigs BinnedContigs HQ BinnedContigs Field_pasture_P2_CheckM_bins.BinnedContigs
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Field_pasture_P2_CheckM_bins.BinnedContigs
    v1 - KBaseMetagenomes.BinnedContigs-1.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Filter Bins by Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
    This app completed without errors in 28m 18s.
    Objects
    Created Object Name Type Description
    Field_pasture_P3_CheckM_bins.BinnedContigs BinnedContigs HQ BinnedContigs Field_pasture_P3_CheckM_bins.BinnedContigs
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Field_pasture_P3_CheckM_bins.BinnedContigs
    v1 - KBaseMetagenomes.BinnedContigs-1.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671
    Filter Bins by Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
    This app completed without errors in 20m 7s.
    Objects
    Created Object Name Type Description
    Field_pasture_P4_CheckM_bins.BinnedContigs BinnedContigs HQ BinnedContigs Field_pasture_P4_CheckM_bins.BinnedContigs
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM
    Field_pasture_P4_CheckM_bins.BinnedContigs
    v1 - KBaseMetagenomes.BinnedContigs-1.0
    The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/159671

    7. MAG extraction and quality assessment

    Extract Bins as Assemblies from BinnedContigs - v1.0.2
    Extract a bin as an Assembly from a BinnedContig dataset
    This app completed without errors in 4m 35s.
    Objects
    Created Object Name Type Description
    Field_forest_FP2_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
    Bin.009.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.006.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.024.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.019.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.003.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.010.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.016.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.022.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.014.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.023.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Bin.001.fastaField_forest_FP2_assembly Assembly Assembly object of extracted contigs
    Summary
    Job Finished Generated Assembly Reference: 159671/1052/4, 159671/1041/4, 159671/1030/4, 159671/1037/4, 159671/1022/4, 159671/1057/4, 159671/1024/4, 159671/1026/4, 159671/1048/4, 159671/1034/4, 159671/1062/4 Generated Assembly Set: 159671/1067/2
    Extract Bins as Assemblies from BinnedContigs - v1.0.2
    Extract a bin as an Assembly from a BinnedContig dataset
    This app completed without errors in 4m 41s.
    Objects
    Created Object Name Type Description
    Field_forest_FP4_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
    Bin.004.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.017.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.015.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.012.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.005.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.002.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.008.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.010.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.001.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.016.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Bin.013.fastaField_forest_FP4_assembly Assembly Assembly object of extracted contigs
    Summary
    Job Finished Generated Assembly Reference: 159671/1028/4, 159671/1047/4, 159671/1061/4, 159671/1056/4, 159671/1023/4, 159671/1039/4, 159671/1051/4, 159671/1025/4, 159671/1036/4, 159671/1032/4, 159671/1045/4 Generated Assembly Set: 159671/1066/2
    Extract Bins as Assemblies from BinnedContigs - v1.0.2
    Extract a bin as an Assembly from a BinnedContig dataset
    This app completed without errors in 2m 30s.
    Objects
    Created Object Name Type Description
    Field_forest_FP5_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
    Bin.001.fastaField_forest_FP5_assembly Assembly Assembly object of extracted contigs
    Bin.003.fastaField_forest_FP5_assembly Assembly Assembly object of extracted contigs
    Bin.005.fastaField_forest_FP5_assembly Assembly Assembly object of extracted contigs
    Bin.002.fastaField_forest_FP5_assembly Assembly Assembly object of extracted contigs
    Summary
    Job Finished Generated Assembly Reference: 159671/1035/4, 159671/1031/4, 159671/1027/4, 159671/1040/4 Generated Assembly Set: 159671/1043/2
    Extract Bins as Assemblies from BinnedContigs - v1.0.2
    Extract a bin as an Assembly from a BinnedContig dataset
    This app completed without errors in 6m 46s.
    Objects
    Created Object Name Type Description
    Field_pasture_P2_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
    Bin.004.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.006.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.019.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.023.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.026.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.017.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.009.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.012.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.024.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.002.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.008.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.007.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.020.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.018.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.028.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.016.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.013.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.014.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.011.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Bin.022.fastaField_pasture_P2_assembly Assembly Assembly object of extracted contigs
    Summary
    Job Finished Generated Assembly Reference: 159671/1074/4, 159671/1079/4, 159671/1088/4, 159671/1090/4, 159671/1058/4, 159671/1096/4, 159671/1084/4, 159671/1092/4, 159671/1094/4, 159671/1033/4, 159671/1063/4, 159671/1100/4, 159671/1053/4, 159671/1070/4, 159671/1029/4, 159671/1049/4, 159671/1077/4, 159671/1042/4, 159671/1099/4, 159671/1038/4 Generated Assembly Set: 159671/1101/2
    Extract Bins as Assemblies from BinnedContigs - v1.0.2
    Extract a bin as an Assembly from a BinnedContig dataset
    This app completed without errors in 5m 24s.
    Objects
    Created Object Name Type Description
    Field_pasture_P3_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
    Bin.004.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.006.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.021.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.017.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.009.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.002.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.008.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.010.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.007.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.020.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.001.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.016.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.013.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.014.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Bin.011.fastaField_pasture_P3_assembly Assembly Assembly object of extracted contigs
    Summary
    Job Finished Generated Assembly Reference: 159671/1082/4, 159671/1095/4, 159671/1078/4, 159671/1050/4, 159671/1059/4, 159671/1071/4, 159671/1089/4, 159671/1091/4, 159671/1064/4, 159671/1093/4, 159671/1044/4, 159671/1054/4, 159671/1081/4, 159671/1075/4, 159671/1086/4 Generated Assembly Set: 159671/1097/2
    Extract Bins as Assemblies from BinnedContigs - v1.0.2
    Extract a bin as an Assembly from a BinnedContig dataset
    This app completed without errors in 3m 23s.
    Objects
    Created Object Name Type Description
    Field_pasture_P4_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
    Bin.001.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.003.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.012.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.010.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.004.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.008.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.002.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Bin.011.fastaField_pasture_P4_assembly Assembly Assembly object of extracted contigs
    Summary
    Job Finished Generated Assembly Reference: 159671/1072/4, 159671/1065/4, 159671/1520/1, 159671/1521/1, 159671/1060/4, 159671/1080/4, 159671/1076/4, 159671/1524/1 Generated Assembly Set: 159671/1085/2
    Build AssemblySet - v1.0.1
    Allows users to create an AssemblySet object.
    This app completed without errors in 28s.
    Objects
    Created Object Name Type Description
    Field_total_AssemblySet AssemblySet KButil_Build_AssemblySet
    Summary
    assembly objs in output set Field_total_AssemblySet: 69
    Assess Genome Quality with CheckM - v1.0.18
    Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
    This app completed without errors in 1h 20m 50s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
    • full_output.zip - Full output of CheckM
    • plots.zip - Output plots from CheckM

    8. Taxonomic classification

    Classify Microbes with GTDB-Tk - v2.3.2
    Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
    This app completed without errors in 2h 20m 1s.
    Objects
    Created Object Name Type Description
    Bin.001.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.003.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.006.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.009.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.010.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.014.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.016.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.019.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.022.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.023.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.024.fastaField_forest_FP2_assembly Assembly Added GTDB lineage
    Bin.001.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.002.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.004.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.005.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.008.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.010.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.012.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.013.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.015.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.016.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.017.fastaField_forest_FP4_assembly Assembly Added GTDB lineage
    Bin.001.fastaField_forest_FP5_assembly Assembly Added GTDB lineage
    Bin.002.fastaField_forest_FP5_assembly Assembly Added GTDB lineage
    Bin.003.fastaField_forest_FP5_assembly Assembly Added GTDB lineage
    Bin.005.fastaField_forest_FP5_assembly Assembly Added GTDB lineage
    Bin.002.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.004.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.006.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.007.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.008.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.009.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.011.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.012.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.013.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.014.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.016.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.017.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.018.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.019.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.020.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.022.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.023.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.024.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.026.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.028.fastaField_pasture_P2_assembly Assembly Added GTDB lineage
    Bin.001.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.002.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.004.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.006.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.007.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.008.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.009.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.010.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.011.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.013.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.014.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.016.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.017.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.020.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.021.fastaField_pasture_P3_assembly Assembly Added GTDB lineage
    Bin.001.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.002.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.003.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.004.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.008.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.010.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.011.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Bin.012.fastaField_pasture_P4_assembly Assembly Added GTDB lineage
    Field_total_AssemblySet AssemblySet Added GTDB lineage
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • gtdbtk.ar53.classify.tree - gtdbtk.ar53.classify.tree - whole tree GTDB formatted Newick
    • gtdbtk.ar53.classify-ITOL.tree - gtdbtk.ar53.classify-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
    • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.bac120.classify.tree.4.tree - gtdbtk.bac120.classify.tree.4.tree - whole tree GTDB formatted Newick
    • gtdbtk.bac120.classify.tree.4-ITOL.tree - gtdbtk.bac120.classify.tree.4-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.bac120.classify.tree.5.tree - gtdbtk.bac120.classify.tree.5.tree - whole tree GTDB formatted Newick
    • gtdbtk.bac120.classify.tree.5-ITOL.tree - gtdbtk.bac120.classify.tree.5-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.bac120.classify.tree.6.tree - gtdbtk.bac120.classify.tree.6.tree - whole tree GTDB formatted Newick
    • gtdbtk.bac120.classify.tree.6-ITOL.tree - gtdbtk.bac120.classify.tree.6-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.bac120.classify.tree.7.tree - gtdbtk.bac120.classify.tree.7.tree - whole tree GTDB formatted Newick
    • gtdbtk.bac120.classify.tree.7-ITOL.tree - gtdbtk.bac120.classify.tree.7-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.bac120.classify.tree.8.tree - gtdbtk.bac120.classify.tree.8.tree - whole tree GTDB formatted Newick
    • gtdbtk.bac120.classify.tree.8-ITOL.tree - gtdbtk.bac120.classify.tree.8-ITOL.tree - whole tree ITOL formatted Newick
    • gtdbtk.ar53.classify-proximals.tree - gtdbtk.ar53.classify-proximals.tree - Newick
    • gtdbtk.ar53.classify-trimmed.tree - gtdbtk.ar53.classify-trimmed.tree - Newick
    • gtdbtk.ar53.classify-lineages.map - gtdbtk.ar53.classify-lineages.map - GTDB lineage
    • gtdbtk.ar53.classify-trimmed.tree-rectangle.PNG - gtdbtk.ar53.classify-trimmed.tree - Image
    • gtdbtk.ar53.classify-trimmed.tree-rectangle.PDF - gtdbtk.ar53.classify-trimmed.tree - Image
    • gtdbtk.ar53.classify-trimmed.tree-circle.PNG - gtdbtk.ar53.classify-trimmed.tree - Image
    • gtdbtk.ar53.classify-trimmed.tree-circle.PDF - gtdbtk.ar53.classify-trimmed.tree - Image
    • gtdbtk.ar53.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.ar53.classify-trimmed.tree - Image
    • gtdbtk.ar53.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.ar53.classify-trimmed.tree - Image
    • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
    • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
    • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
    • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
    • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
    • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
    • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
    • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
    • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.4-proximals.tree - gtdbtk.bac120.classify.tree.4-proximals.tree - Newick
    • gtdbtk.bac120.classify.tree.4-trimmed.tree - gtdbtk.bac120.classify.tree.4-trimmed.tree - Newick
    • gtdbtk.bac120.classify.tree.4-lineages.map - gtdbtk.bac120.classify.tree.4-lineages.map - GTDB lineage
    • gtdbtk.bac120.classify.tree.4-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.4-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.5-proximals.tree - gtdbtk.bac120.classify.tree.5-proximals.tree - Newick
    • gtdbtk.bac120.classify.tree.5-trimmed.tree - gtdbtk.bac120.classify.tree.5-trimmed.tree - Newick
    • gtdbtk.bac120.classify.tree.5-lineages.map - gtdbtk.bac120.classify.tree.5-lineages.map - GTDB lineage
    • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.6-proximals.tree - gtdbtk.bac120.classify.tree.6-proximals.tree - Newick
    • gtdbtk.bac120.classify.tree.6-trimmed.tree - gtdbtk.bac120.classify.tree.6-trimmed.tree - Newick
    • gtdbtk.bac120.classify.tree.6-lineages.map - gtdbtk.bac120.classify.tree.6-lineages.map - GTDB lineage
    • gtdbtk.bac120.classify.tree.6-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.6-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.6-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.6-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.6-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.6-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.6-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.6-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.6-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.6-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.6-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.6-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.7-proximals.tree - gtdbtk.bac120.classify.tree.7-proximals.tree - Newick
    • gtdbtk.bac120.classify.tree.7-trimmed.tree - gtdbtk.bac120.classify.tree.7-trimmed.tree - Newick
    • gtdbtk.bac120.classify.tree.7-lineages.map - gtdbtk.bac120.classify.tree.7-lineages.map - GTDB lineage
    • gtdbtk.bac120.classify.tree.7-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.7-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.7-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.7-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.7-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.7-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.7-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.7-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.7-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.7-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.7-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.7-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.8-proximals.tree - gtdbtk.bac120.classify.tree.8-proximals.tree - Newick
    • gtdbtk.bac120.classify.tree.8-trimmed.tree - gtdbtk.bac120.classify.tree.8-trimmed.tree - Newick
    • gtdbtk.bac120.classify.tree.8-lineages.map - gtdbtk.bac120.classify.tree.8-lineages.map - GTDB lineage
    • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
    • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
    • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output

    9. ANI comparisons

    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 1m 0s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 42s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 1m 6s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 56s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 43s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 48s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 1m 0s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 43s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 53s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 45s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 47s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 51s.
    Report
    Links
    Compute ANI with FastANI
    Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
    This app completed without errors in 50s.
    Report
    Links

    10. Functional annotation

    Annotate and Distill Assemblies with DRAM
    Annotate your assemblies, isolate genomes, or MAGs with DRAM and distill resulting annotations to create an interactive functional summary per genome or assembly. Use for KBase assembly objects.
    This app completed without errors in 2d 0h 20m 24s.
    Objects
    Created Object Name Type Description
    Bin.001.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.001.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.001.fastaField_forest_FP5_assembly_DRAM Genome Annotated Genome
    Bin.001.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.001.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.002.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.002.fastaField_forest_FP5_assembly_DRAM Genome Annotated Genome
    Bin.002.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.002.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.002.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.003.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.003.fastaField_forest_FP5_assembly_DRAM Genome Annotated Genome
    Bin.003.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.004.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.004.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.004.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.004.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.005.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.005.fastaField_forest_FP5_assembly_DRAM Genome Annotated Genome
    Bin.006.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.006.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.006.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.007.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.007.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.008.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.008.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.008.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.008.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.009.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.009.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.009.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.010.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.010.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.010.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.010.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.011.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.011.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.011.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.012.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.012.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.012.fastaField_pasture_P4_assembly_DRAM Genome Annotated Genome
    Bin.013.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.013.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.013.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.014.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.014.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.014.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.015.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.016.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.016.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.016.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.016.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.017.fastaField_forest_FP4_assembly_DRAM Genome Annotated Genome
    Bin.017.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.017.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.018.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.019.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.019.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.020.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.020.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.021.fastaField_pasture_P3_assembly_DRAM Genome Annotated Genome
    Bin.022.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.022.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.023.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.023.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.024.fastaField_forest_FP2_assembly_DRAM Genome Annotated Genome
    Bin.024.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.026.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Bin.028.fastaField_pasture_P2_assembly_DRAM Genome Annotated Genome
    Field_total_DRAM GenomeSet Forest and pasture MAGs
    Report
    Summary
    Here are the results from your DRAM run.
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • annotations.tsv - DRAM annotations in a tab separate table format
    • genes.fna - Genes as nucleotides predicted by DRAM with brief annotations
    • genes.faa - Genes as amino acids predicted by DRAM with brief annotations
    • genes.gff - GFF file of all DRAM annotations
    • rrnas.tsv - Tab separated table of rRNAs as detected by barrnap
    • trnas.tsv - Tab separated table of tRNAs as detected by tRNAscan-SE
    • genbank.tar.gz - Compressed folder of output genbank files
    • product.tsv - DRAM product in tabular format
    • metabolism_summary.xlsx - DRAM metabolism summary tables
    • genome_stats.tsv - DRAM genome statistics table
    Search with HMMs of MicroTrait Bioelement families - v1
    Search for matches to HMMs of MicroTrait environmental bioelement cycling families using HMMER 3
    This app completed without errors in 7m 19s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • HMMER_MT_Bioelement_Search.TAB.zip
    Search with dbCAN2 HMMs of CAZy families - v10
    Search for matches to dbCAN HMMs of CAZy carbohydrate active enzyme families using HMMER 3
    This app completed without errors in 14m 48s.
    Report
    Links
    Files
    These are only available in the live Narrative: https://narrative.kbase.us/narrative/159671
    • HMMER_dbCAN_Search.TAB.zip

    11. Coverage calculation for high-quality MAGs

    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 21h 49m 2s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 20h 18m 30s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 50m 33s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 19m 13s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 22h 36m 50s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 16h 56m 13s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 13m 10s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 12m 25s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 37m 35s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 16m 23s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 5m 5s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 38m 11s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 58m 48s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 48m 36s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 47m 20s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 6m 49s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 58m 29s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 32m 46s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 47m 42s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 56m 14s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 23m 51s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 21h 42m 54s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 50m 48s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 56m 58s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 34m 18s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 0m 17s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 12h 24m 56s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 12m 24s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 0m 37s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 42m 36s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 16h 49m 40s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 15m 32s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 5m 51s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 48m 5s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 12h 7m 46s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 0m 33s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 12h 41m 41s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 18m 6s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 11h 49m 16s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 53m 52s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 12h 59m 56s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 44m 55s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 12h 2m 15s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 48m 33s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 53m 56s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 12h 26m 15s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 48m 39s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 9m 53s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 16h 7m 25s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 32m 47s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 12m 30s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 18h 15m 9s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 53m 13s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 0m 43s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 13h 29m 29s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 58m 9s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 24m 11s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 51m 37s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 56m 9s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 15h 53m 38s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 14h 55m 19s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 30m 12s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 46m 16s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 57m 5s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 16h 43m 33s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 51m 60s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 19h 3m 48s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 35m 0s.
    No output found.
    Align Reads using Bowtie2 - v2.3.2
    Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
    This app completed without errors in 17h 38m 25s.
    No output found.

    Apps

    1. Align Reads using Bowtie2 - v2.3.2
      • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9: 357 359. doi:10.1038/nmeth.1923
      • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi:10.1186/gb-2009-10-3-r25
    2. Annotate and Distill Assemblies with DRAM
      • DRAM source code
      • DRAM documentation
      • DRAM Tutorial
      • DRAM publication
    3. Assemble Reads with MEGAHIT v1.2.9
      • Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31: 1674 1676. doi:10.1093/bioinformatics/btv033
    4. Assess Genome Quality with CheckM - v1.0.18
      • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114
      • CheckM source:
      • Additional info:
    5. Assess Quality of Assemblies with QUAST - v4.4
      • [1] Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29: 1072 1075. doi:10.1093/bioinformatics/btt086
      • [2] Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A. Icarus: visualizer for de novo assembly evaluation. Bioinformatics. 2016;32: 3321 3323. doi:10.1093/bioinformatics/btw379
    6. Assess Read Quality with FastQC - v0.12.1
      • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
    7. Bin Contigs using CONCOCT - v1.1
      • Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C. Binning metagenomic contigs by coverage and composition. Nature Methods. 2014;11: 1144-1146. doi:10.1038/nmeth.3103
      • CONCOCT source:
    8. Bin Contigs using MaxBin2 - v2.2.4
      • Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32: 605 607. doi:10.1093/bioinformatics/btv638 (2) 1. Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2: 26. doi:10.1186/2049-2618-2-26
      • Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2: 26. doi:10.1186/2049-2618-2-26
      • Maxbin2 source:
      • Maxbin source:
    9. Build AssemblySet - v1.0.1
      • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
      • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
    10. Build ReadsSet - v1.7.6
      • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
      • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
    11. Classify Microbes with GTDB-Tk - v2.3.2
      • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, Volume 38, Issue 23, 1 December 2022, Pages 5315 5316. DOI: https://doi.org/10.1093/bioinformatics/btac672
      • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks, GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, Volume 36, Issue 6, 15 March 2020, Pages 1925 1927. DOI: https://doi.org/10.1093/bioinformatics/btz848
      • Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D785 D794. DOI: https://doi.org/10.1093/nar/gkab776
      • Parks, D., Chuvochina, M., Waite, D. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36, 996 1004 (2018). DOI: https://doi.org/10.1038/nbt.4229
      • Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;10.1038/s41587-020-0501-8. DOI:10.1038/s41587-020-0501-8
      • Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Dav n AA, Waite DW, Whitman WB, Parks DH, and Hugenholtz P. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol. 2021 Jul;6(7):946-959. DOI:10.1038/s41564-021-00918-8
      • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
      • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010;11:538. Published 2010 Oct 30. doi:10.1186/1471-2105-11-538
      • Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114. Published 2018 Nov 30. DOI:10.1038/s41467-018-07641-9
      • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. Published 2010 Mar 8. DOI:10.1186/1471-2105-11-119
      • Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. Published 2010 Mar 10. DOI:10.1371/journal.pone.0009490 link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835736/
      • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7(10):e1002195. DOI:10.1371/journal.pcbi.1002195
      • Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132. DOI: 10.1186/s13059-016-0997-x
    12. Compute ANI with FastANI
      • [1] Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries. 2017; doi:10.1101/225342
      • [2] Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57: 81 91. doi:10.1099/ijs.0.64483-0
      • FastANI module and source code:
    13. Extract Bins as Assemblies from BinnedContigs - v1.0.2
      • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
    14. Filter Bins by Quality with CheckM - v1.0.18
      • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114
      • CheckM source:
      • Additional info:
    15. Merge Reads Libraries - v1.2.2
      • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
    16. MetaBAT2 Contig Binning - v1.7
      • Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3: e1165. doi:10.7717/peerj.1165
      • MetaBAT2 source:
    17. Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
      • Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. 2018; 3(7): 836-843. doi:10.1038/s41564-018-0171-1
      • DAS_Tool source:
      • Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
      • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10: 421. doi:10.1186/1471-2105-10-421
      • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nature Methods. 2015;12: 59-60. doi:10.1038/nmeth.3176
      • Pullseq:
      • R: A Language and Environment for Statistical Computing:
      • Ruby: A Programmers Best Friend:
    18. Search with dbCAN2 HMMs of CAZy families - v10
      • Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101. doi: 10.1093/nar/gky418
      • Eddy SR. Accelerated Profile HMM Searches. PLOS Computational Biology. 2011;7: e1002195. doi:10.1371/journal.pcbi.1002195
      • HMMER v3.3.2 source:
      • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
    19. Search with HMMs of MicroTrait Bioelement families - v1
      • Karaoz U, Brodie EL. microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes. Front Bioinform. 2022 Jul 22;2:918853. doi: 10.3389/fbinf.2022.918853
      • Eddy SR. Accelerated Profile HMM Searches. PLOS Computational Biology. 2011;7: e1002195. doi:10.1371/journal.pcbi.1002195
      • HMMER v3.3.2 source:
      • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
    20. Trim Reads with Trimmomatic - v0.36
      • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114 2120. doi:10.1093/bioinformatics/btu170