Metagenome-assembled Genome Sequences Recovered from Epilithic River Biofilm in Tama River, Japan
Joval Martinez
Generated August 3, 2021

Welcome to KBase's Narrative Interface!

What's a Narrative? Narratives are shareable, reproducible workflows that can include data, analysis steps, results, visualizations and commentary. Learn more...

Take the Tour: Choose "Narrative Tour" from the "Help" menu above. The tour walks you through the user interface, pointing out various useful aspects of it.

Get Some Data: Click the Add Data button in the Data Panel to search KBase data or upload your own. Hover over a data object to reveal a button for adding it to your Narrative. Learn more...

Analyze It: Use the Apps panel or the App Catalog to browse available analysis apps. Select an app to add it to your Narrative, fill in the fields, and click the "Run" button to launch the app. Learn more...

Save and Share Your Narrative: Be sure to save your Narrative frequently. To let collaborators view your analysis steps and results, click the Share button. Or make your Narrative public and help expand the social web that KBase is building to make systems biology research more open, reproducible and collaborative. Learn more...

Find Documentation: For more information, please see the Narrative Interface User Guide or the tutorials.

Questions? Bug reports? Contact us!

Ready to begin adding to your Narrative? You can keep this Welcome cell or delete it by selecting "Delete cell" from the "..." menu in the top right corner of this cell.

METAGENOME RECOVERED FROM RIVER BIOFILM

1. READ HYGIENE

Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 8m 10s.
Objects
Created Object Name Type Description
001_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 8m 11s.
Objects
Created Object Name Type Description
002_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 15m 41s.
Objects
Created Object Name Type Description
004_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 52s.
Objects
Created Object Name Type Description
003_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 13m 12s.
Objects
Created Object Name Type Description
005_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 5m 40s.
Objects
Created Object Name Type Description
006_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 26m 22s.
Objects
Created Object Name Type Description
007_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 5m 37s.
Objects
Created Object Name Type Description
008_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 5m 37s.
Objects
Created Object Name Type Description
009_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 8m 12s.
Objects
Created Object Name Type Description
010_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 5m 36s.
Objects
Created Object Name Type Description
011_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 2m 51s.
Objects
Created Object Name Type Description
012_Ig3554.fastq.gz_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 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/95585
  • 001_Ig3554.fastq.gz_reads_74188_2_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 001_Ig3554.fastq.gz_reads_74188_2_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 5m 20s.
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/95585
  • 002_Ig3554.fastq.gz_reads_74188_4_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 002_Ig3554.fastq.gz_reads_74188_4_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 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/95585
  • 003_Ig3554.fastq.gz_reads_74188_6_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 003_Ig3554.fastq.gz_reads_74188_6_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 11m 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/95585
  • 004_Ig3554.fastq.gz_reads_74188_7_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 004_Ig3554.fastq.gz_reads_74188_7_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 38s.
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/95585
  • 005_Ig3554.fastq.gz_reads_74188_11_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 005_Ig3554.fastq.gz_reads_74188_11_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 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/95585
  • 006_Ig3554.fastq.gz_reads_74188_10_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 006_Ig3554.fastq.gz_reads_74188_10_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 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/95585
  • 007_Ig3554.fastq.gz_reads_74188_24_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 007_Ig3554.fastq.gz_reads_74188_24_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 38s.
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/95585
  • 008_Ig3554.fastq.gz_reads_74188_14_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 008_Ig3554.fastq.gz_reads_74188_14_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 38s.
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/95585
  • 009_Ig3554.fastq.gz_reads_74188_16_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 009_Ig3554.fastq.gz_reads_74188_16_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 5m 12s.
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/95585
  • 010_Ig3554.fastq.gz_reads_74188_20_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 010_Ig3554.fastq.gz_reads_74188_20_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 9m 27s.
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/95585
  • 011_Ig3554.fastq.gz_reads_74188_21_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 011_Ig3554.fastq.gz_reads_74188_21_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 38s.
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/95585
  • 012_Ig3554.fastq.gz_reads_74188_18_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 012_Ig3554.fastq.gz_reads_74188_18_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report

2. TAXONOMIC CLASSIFICATION OF READS

Classify Taxonomy of Metagenomic Reads with GOTTCHA2 - v2.1.6
Uses GOTTCHA2 to provide taxonomic classifications of shotgun metagenomic reads data.
This app completed without errors in 43m 17s.
Report
Summary
GOTTCHA2 run finished on cf45d9aa-dda5-4f16-9662-0a65cee9ecb3.inter.fastq.gz,72b543a9-55d7-4d5a-b4d5-b1de40eb53c4.inter.fastq.gz,38c676ae-4ff1-4d73-901e-de0dfcedc07b.inter.fastq.gz,a71359b3-3a27-401d-b93c-427433f120bb.inter.fastq.gz,49ffe9f6-8f4c-4856-8d0c-3d6cd81ebd5c.inter.fastq.gz,b5794f7b-ecf9-4909-bded-11c41753e476.inter.fastq.gz,1b893bae-557b-4c3a-836e-5c04d1e864a5.inter.fastq.gz,56d84d4c-2491-4f71-a4b2-e9ae4d4f3b99.inter.fastq.gz,18ce9ab4-ae9e-4db3-b508-2c660df46861.inter.fastq.gz,ad79d84c-1d4f-4dc8-a733-20f63ba9f6c8.inter.fastq.gz,424a53d7-356b-4855-a223-db8402c77a8c.inter.fastq.gz,56f6c88d-4ddf-4e26-9a4d-e1e07df6e891.inter.fastq.gz against RefSeq-r90.cg.BacteriaArchaeaViruses.species.fna.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • gottcha2.lineage.tsv
  • html_report
  • gottcha2.tsv
  • gottcha2.gottcha_species.log
  • gottcha2.gottcha_species.sam
  • gottcha2.out.tab_tree
  • gottcha2.full.tsv
  • gottcha2.krona.html
  • gottcha2.out.list
  • gottcha2.summary.tsv
Classify Taxonomy of Metagenomic Reads with Kaiju - v1.7.3
Allows users to perform taxonomic classification of shotgun metagenomic read data with Kaiju.
This app completed without errors in 1h 14m 20s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • kaiju_classifications.zip
  • kaiju_summaries.zip
  • krona_data.zip
  • stacked_bar_abundance_plots_PNG+PDF.zip

3. METAGENOME ASSEMBLY

Import FASTA File as Assembly from Staging Area
Import a FASTA file from your staging area into your Narrative as an Assembly data object
This app completed without errors in 1m 46s.
Objects
Created Object Name Type Description
Ig3554_meta-velvetg.contigs.fa_assembly Assembly Imported Assembly
Report
Links
  • report.html - HTML summary report for Imported Assembly
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 2m 7s.
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 Ig3554_meta-velvetg.contigs.fa_assembly # contigs (>= 0 bp) 9 # contigs (>= 1000 bp) 8 # contigs (>= 10000 bp) 2 # contigs (>= 100000 bp) 0 # contigs (>= 1000000 bp) 0 Total length (>= 0 bp) 42502 Total length (>= 1000 bp) 41598 Total length (>= 10000 bp) 25061 Total length (>= 100000 bp) 0 Total length (>= 1000000 bp) 0 # contigs 9 Largest contig 12955 Total length 42502 GC (%) 48.49 N50 12106 N75 3919 L50 2 L75 4 # N's per 100 kbp 352.92 # predicted genes (unique) 26 # predicted genes (>= 0 bp) 24 + 2 part # predicted genes (>= 300 bp) 22 + 1 part # predicted genes (>= 1500 bp) 6 + 0 part # predicted genes (>= 3000 bp) 1 + 0 part
Links
Merge Reads Libraries - v1.0.1
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 58m 10s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib.reads PairedEndLibrary Merged Ig3554 to one Library Reads
Summary
NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 12
Output from Merge Reads Libraries - v1.0.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/95585
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 21m 15s.
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/95585
  • Ig3554_merged_Lib.reads_74188_40_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Ig3554_merged_Lib.reads_74188_40_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 3m 48s.
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/95585
  • 001_Ig3554.fastq.gz_reads_74188_2_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • 001_Ig3554.fastq.gz_reads_74188_2_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 36m 52s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_paired PairedEndLibrary Trimmed Reads
Ig3554_merged_Lib_Trimm_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
Ig3554_merged_Lib_Trimm_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Report
Links
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 21m 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/95585
  • Ig3554_merged_Lib_Trimm_paired_74188_45_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Ig3554_merged_Lib_Trimm_paired_74188_45_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assemble Reads with metaSPAdes - v3.13.0
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 4h 49m 36s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_unpaired_SPAdes.contigs Assembly Assembled contigs
Report
Summary
Assembly saved to: joval:narrative_1602053741718/SPAdes.contigs Assembled into 45103 contigs. Avg Length: 5563.775957253398 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 44952 -- 2000.0 to 62737.0 bp 124 -- 62737.0 to 123474.0 bp 15 -- 123474.0 to 184211.0 bp 5 -- 184211.0 to 244948.0 bp 5 -- 244948.0 to 305685.0 bp 0 -- 305685.0 to 366422.0 bp 0 -- 366422.0 to 427159.0 bp 1 -- 427159.0 to 487896.0 bp 0 -- 487896.0 to 548633.0 bp 1 -- 548633.0 to 609370.0 bp
Links
Assemble Reads with metaSPAdes - v3.13.0
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 1h 7m 41s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_SPAdes.contigs Assembly Assembled contigs
Report
Summary
Assembly saved to: joval:narrative_1602053741718/Ig3554_merged_Lib_Trimm_SPAdes.contigs Assembled into 44792 contigs. Avg Length: 5541.2497544204325 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 44687 -- 2000.0 to 71679.0 bp 86 -- 71679.0 to 141358.0 bp 11 -- 141358.0 to 211037.0 bp 4 -- 211037.0 to 280716.0 bp 2 -- 280716.0 to 350395.0 bp 0 -- 350395.0 to 420074.0 bp 0 -- 420074.0 to 489753.0 bp 0 -- 489753.0 to 559432.0 bp 1 -- 559432.0 to 629111.0 bp 1 -- 629111.0 to 698790.0 bp
Links
Assemble Reads with MEGAHIT v1.2.9
Assemble metagenomic reads using the MEGAHIT assembler.
This app completed without errors in 4h 43m 19s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_MEGAHIT.assembly Assembly Assembled contigs
Report
Summary
ContigSet saved to: joval:narrative_1602053741718/Ig3554_merged_Lib_MEGAHIT.assembly Assembled into 43558 contigs. Avg Length: 5143.289567932412 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 43483 -- 2000.0 to 69797.6 bp 56 -- 69797.6 to 137595.2 bp 9 -- 137595.2 to 205392.80000000002 bp 3 -- 205392.80000000002 to 273190.4 bp 3 -- 273190.4 to 340988.0 bp 0 -- 340988.0 to 408785.60000000003 bp 0 -- 408785.60000000003 to 476583.20000000007 bp 3 -- 476583.20000000007 to 544380.8 bp 0 -- 544380.8 to 612178.4 bp 1 -- 612178.4 to 679976.0 bp
Links
Assemble Reads with MEGAHIT v1.2.9
Assemble metagenomic reads using the MEGAHIT assembler.
This app completed without errors in 4h 55m 57s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_paired_MEGAHIT.assembly Assembly Assembled contigs
Report
Summary
ContigSet saved to: joval:narrative_1602053741718/Ig3554_merged_Lib_Trimm_paired_MEGAHIT.assembly Assembled into 43131 contigs. Avg Length: 5125.549859729661 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 43063 -- 2000.0 to 73862.6 bp 48 -- 73862.6 to 145725.2 bp 9 -- 145725.2 to 217587.80000000002 bp 7 -- 217587.80000000002 to 289450.4 bp 2 -- 289450.4 to 361313.0 bp 0 -- 361313.0 to 433175.60000000003 bp 1 -- 433175.60000000003 to 505038.20000000007 bp 0 -- 505038.20000000007 to 576900.8 bp 0 -- 576900.8 to 648763.4 bp 1 -- 648763.4 to 720626.0 bp
Links
Assemble Reads with IDBA-UD - v1.1.3
Assemble paired-end reads from single-cell or metagenomic sequencing technologies using the IDBA-UD assembler.
This app completed without errors in 16h 36m 1s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_IDBA.contigs Assembly Assembled contigs
Report
Summary
Assembly saved to: joval:narrative_1602053741718/Ig3554_merged_Lib_Trimm_IDBA.contigs Assembled into 23814 contigs. Avg Length: 4999.50415722 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 23529 -- 2001.0 to 29093.8 bp 189 -- 29093.8 to 56186.6 bp 55 -- 56186.6 to 83279.4 bp 21 -- 83279.4 to 110372.2 bp 6 -- 110372.2 to 137465.0 bp 7 -- 137465.0 to 164557.8 bp 3 -- 164557.8 to 191650.6 bp 1 -- 191650.6 to 218743.4 bp 2 -- 218743.4 to 245836.2 bp 1 -- 245836.2 to 272929.0 bp
Links
Compare Assembled Contig Distributions - v1.1.2
View distributions of contig characteristics for different assemblies.
This app completed without errors in 4m 32s.
Report
Summary
ASSEMBLY STATS for Ig3554_merged_Lib_Trimm_paired_MEGAHIT.assembly Len longest contig: 720626 bp N50 (L50): 6006 (8634) N75 (L75): 3311 (21290) N90 (L90): 2425 (33068) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 37 Num contigs >= 10000 bp: 3568 Num contigs >= 1000 bp: 43131 Num contigs >= 500 bp: 43131 Num contigs >= 1 bp: 43131 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 7261176 bp Len contigs >= 10000 bp: 72081064 bp Len contigs >= 1000 bp: 221070091 bp Len contigs >= 500 bp: 221070091 bp Len contigs >= 1 bp: 221070091 bp ASSEMBLY STATS for Ig3554_merged_Lib_Trimm_SPAdes.contigs Len longest contig: 698790 bp N50 (L50): 6989 (7695) N75 (L75): 3481 (20714) N90 (L90): 2457 (33561) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 49 Num contigs >= 10000 bp: 4507 Num contigs >= 1000 bp: 44792 Num contigs >= 500 bp: 44792 Num contigs >= 1 bp: 44792 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 8225847 bp Len contigs >= 10000 bp: 97771859 bp Len contigs >= 1000 bp: 248203659 bp Len contigs >= 500 bp: 248203659 bp Len contigs >= 1 bp: 248203659 bp ASSEMBLY STATS for Ig3554_merged_Lib_Trimm_IDBA.contigs Len longest contig: 272929 bp N50 (L50): 5401 (4984) N75 (L75): 3233 (12291) N90 (L90): 2494 (18603) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 26 Num contigs >= 10000 bp: 1500 Num contigs >= 1000 bp: 23814 Num contigs >= 500 bp: 23814 Num contigs >= 1 bp: 23814 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 3909140 bp Len contigs >= 10000 bp: 35067440 bp Len contigs >= 1000 bp: 119058192 bp Len contigs >= 500 bp: 119058192 bp Len contigs >= 1 bp: 119058192 bp
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • key_plot.png
  • key_plot.pdf
  • cumulative_len_plot.png
  • cumulative_len_plot.pdf
  • sorted_contig_lengths.png
  • sorted_contig_lengths.pdf
  • histogram_figures.zip
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 3m 36s.
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 Ig3554_merged_Lib_Trimm_SPAdes.contigs # contigs (>= 0 bp) 44792 # contigs (>= 1000 bp) 44792 # contigs (>= 10000 bp) 4507 # contigs (>= 100000 bp) 49 # contigs (>= 1000000 bp) 0 Total length (>= 0 bp) 248203659 Total length (>= 1000 bp) 248203659 Total length (>= 10000 bp) 97771859 Total length (>= 100000 bp) 8225847 Total length (>= 1000000 bp) 0 # contigs 44792 Largest contig 698790 Total length 248203659 GC (%) 48.01 N50 6989 N75 3481 L50 7695 L75 20714 # N's per 100 kbp 358.58
Links

4. Bin Contigs

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 1h 59m 51s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • concoct_result.zip - Files generated by CONCOCT App

5. Assess Quality of Bin Contigs

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 22m 15s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • 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 13s.
Objects
Created Object Name Type Description
Ig3554_Trimm_SPAdes_CheckM_HQ_16bins_90comp_2cont.BinnedContigs BinnedContigs HQ BinnedContigs Ig3554_Trimm_SPAdes_CheckM_HQ_16bins_90comp_2cont.BinnedContigs
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Extract Bins as Assemblies - v1.0.2
Extract a bin as an Assembly object from a BinnedContig object dataset.
This app completed without errors in 5m 21s.
Objects
Created Object Name Type Description
Ig3554_Trimm_SPAdes_CheckM_HQ_extracted_7bins_90comp_2cont.AssemblySet AssemblySet Assembly set of extracted assemblies
Bin.090.fasta_assembly Assembly Assembly object of extracted contigs
Bin.061.fasta_assembly Assembly Assembly object of extracted contigs
Bin.056.fasta_assembly Assembly Assembly object of extracted contigs
Bin.053.fasta_assembly Assembly Assembly object of extracted contigs
Bin.082.fasta_assembly Assembly Assembly object of extracted contigs
Bin.044.fasta_assembly Assembly Assembly object of extracted contigs
Bin.050.fasta_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 74188/124/1, 74188/125/1, 74188/76/2, 74188/126/1, 74188/127/1, 74188/128/1, 74188/129/1 Generated Assembly Set: 74188/130/1
Extract Bins as Assemblies - v1.0.2
Extract a bin as an Assembly object from a BinnedContig object dataset.
This app completed without errors in 12m 59s.
Objects
Created Object Name Type Description
Ig3554_extracted_16bins.AssemblySet AssemblySet Assembly set of extracted assemblies
bin.061.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.028.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.088.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.024.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.044.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.030.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.013.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.056.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.009.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.053.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.090.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.085.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.082.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.081.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.050.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
bin.000.fastaIg3554_Trimm_dastool_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 74188/191/1, 74188/192/1, 74188/193/1, 74188/194/1, 74188/195/1, 74188/196/1, 74188/197/1, 74188/198/1, 74188/199/1, 74188/200/1, 74188/201/1, 74188/202/1, 74188/203/1, 74188/204/1, 74188/205/1, 74188/206/1 Generated Assembly Set: 74188/207/1
Extract Bins as Assemblies from BinnedContigs - v1.0.2
Extract a bin as an Assembly from a BinnedContig dataset
This app is new, and hasn't been started.
No output found.

6. Annotate Genome/Assembly

Annotate Metagenome Assembly with Prokka - v1.14.5
Annotate Metagenome Assembly with Prokka annotation pipeline.
This app completed without errors in 4h 14m 49s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_SPAdes_Prokka.annotatedmetagenome AnnotatedMetagenomeAssembly Annotated Metagenome Assembly
Summary
Annotated Metagenome Assembly saved to: joval:narrative_1602053741718/Ig3554_merged_Lib_Trimm_SPAdes_Prokka.annotatedmetagenome
Annotate Metagenome Assembly and Re-annotate Metagenomes with Prokka(v1.12)
Annotate Metagenome Assembly and Re-annotate Metagenomes with Prokka annotation pipeline.
This app completed without errors in 3h 30m 43s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_Spades_MetaAnnotate_RAStk.annotation AnnotatedMetagenomeAssembly Annotated Metagenome Assembly
Summary
Annotated Metagenome Assembly saved to: joval:narrative_1602053741718/Ig3554_merged_Lib_Trimm_Spades_MetaAnnotate_RAStk.annotation
Annotate Domains in a GenomeSet
Annotate domains in every Genome within a GenomeSet using protein domains from widely used domain libraries.
This app completed without errors in 15h 42m 19s.
Summary
Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1 Search Domains output: Getting DomainModelSet from storage. Getting Genome from storage. Running domain search against library 2959/35/1 Running domain search against library 2959/18/2 Running domain search against library 2959/24/2 Running domain search against library 2959/25/2 Running domain search against library 2959/39/1 Running domain search against library 2959/7/8 Running domain search against library 2959/36/1 Running domain search against library 2959/34/1 Running domain search against library 2959/37/1 Running domain search against library 2959/38/1

7. Taxonomic Classification of MAGS

GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 37m 37s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 58m 0s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 28m 14s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 1h 14m 28s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 26m 37s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 24m 34s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 40m 32s.
Report
Links
GTDB-Tk classify
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver 1.1.0
This app completed without errors in 41m 55s.
Report
Links

8. Compute ANI

Compute ANI with FastANI
Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
This app completed without errors in 13m 35s.
Report
Links

9. Construct Species Tree

Build Microbial SpeciesTree - v1.6.0
Build Species Tree for your Microbial Genomes, optionally including Tree Skeleton of Phylum Exemplars
This app completed without errors in 36m 24s.
Objects
Created Object Name Type Description
Ig3554_extracted_16bins.SpeciesTree Tree None
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • Ig3554_extracted_16bins.SpeciesTree.newick
  • Ig3554_extracted_16bins.SpeciesTree-labels.newick
  • Ig3554_extracted_16bins.SpeciesTree.png
  • Ig3554_extracted_16bins.SpeciesTree.pdf

10. Annotate and Distill Metagenome

Annotate and Distill Assemblies with DRAM
Annotate your assembly with DRAM. Annotations will then be distilled to create an interactive functional summary per assembly.
This app completed without errors in 3h 13m 20s.
Objects
Created Object Name Type Description
Bin.044.fasta_assembly_genome Genome Annotated Genome
Bin.050.fasta_assembly_genome Genome Annotated Genome
Bin.053.fasta_assembly_genome Genome Annotated Genome
Bin.056.fasta_assembly_genome Genome Annotated Genome
Bin.061.fasta_assembly_genome Genome Annotated Genome
Bin.082.fasta_assembly_genome Genome Annotated Genome
Bin.090.fasta_assembly_genome Genome Annotated Genome
Ig3554_HQ_7bins_2cont.GenomeSet GenomeSet 7 HQ Bins from Ig3554 Metagenome with > 90% completeness and <2% contamination
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/95585
  • 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
Annotate and Distill Assemblies with DRAM
Annotate your assembly with DRAM. Annotations will then be distilled to create an interactive functional summary per assembly.
This app completed without errors in 7h 15m 27s.
Objects
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/95585
  • 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

11. Build and Compute Pangenome

Build Pangenome with OrthoMCL - v2.0
Create a Pangenome object by performing OrthoMCL orthologous groups construction on a set of Genomes.
This app completed without errors in 2h 15m 55s.
Objects
Created Object Name Type Description
Ig3554_extracted_16bins.Pangenome Pangenome Pangenome object
Summary
Input genomes: 16 Output orthologs: 23534
Phylogenetic Pangenome Accumulation - v1.4.0
View a Pangenome in a phylogenetic context.
This app completed without errors in 8m 22s.
Objects
Created Object Name Type Description
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-0.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-0 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-0.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-0 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-1.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-1 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-1.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-1 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-1.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-1 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-2.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-2 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-2.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-2 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-3.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-3 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-3.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-3 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-3.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-3 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-4.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-4 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-4.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-4 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-4.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-4 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-5.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-5 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-5.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-5 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-6.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-6 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-6.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-6 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-6.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-6 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-7.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-7 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-7.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-7 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-8.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-8 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-8.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-8 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-9.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-9 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-9.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-9 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-9.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-9 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-10.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-10 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-10.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-10 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-11.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-11 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-11.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-11 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-11.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-11 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-12.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-12 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-12.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-12 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-12.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-12 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-13.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-13 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-13.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-13 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-13.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-13 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-14.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-14 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-14.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-14 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-14.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-14 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-15.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-15 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-15.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-15 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-15.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-15 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-16.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-16 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-16.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-16 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-16.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-16 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-17.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-17 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-17.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-17 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-18.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-18 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-18.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-18 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-18.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-18 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-19.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-19 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-19.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-19 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-19.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-19 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-20.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-20 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-20.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-20 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-21.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-21 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-21.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-21 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-21.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-21 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-22.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-22 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-22.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-22 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-23.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-23 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-23.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-23 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-23.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-23 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-24.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-24 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-24.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-24 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-24.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-24 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-25.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-25 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-25.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-25 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-26.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-26 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-26.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-26 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-26.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-26 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-27.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-27 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-27.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-27 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-27.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-27 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-28.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-28 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-28.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-28 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-28.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-28 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-29.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-29 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-29.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-29 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-29.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-29 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-30.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-30 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-30.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-30 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-31.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-31 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-31.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-31 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-31.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-31 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-32.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-32 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-32.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-32 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-33.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-33 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-33.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-33 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-33.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-33 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-34.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-34 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-34.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-34 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-35.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-35 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-35.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-35 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-36.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-36 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-36.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-36 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-36.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-36 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-37.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-37 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-37.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-37 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-37.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-37 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-38.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-38 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-38.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-38 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-39.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-39 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-39.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-39 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-39.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-39 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-40.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-40 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-40.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-40 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-41.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-41 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-41.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-41 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-41.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-41 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-42.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-42 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-42.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-42 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-43.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-43 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-43.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-43 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-43.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-43 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-44.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-44 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-44.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-44 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-44.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-44 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-45.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-45 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-45.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-45 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-45.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-45 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-46.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-46 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-46.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-46 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-47.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-47 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-47.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-47 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-47.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-47 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-48.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-48 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-48.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-48 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-49.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-49 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-49.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-49 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-49.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-49 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-50.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-50 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-50.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-50 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-51.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-51 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-51.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-51 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-51.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-51 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-52.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-52 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-52.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-52 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-52.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-52 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-53.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-53 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-53.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-53 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-53.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-53 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-54.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-54 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-54.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-54 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-54.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-54 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-55.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-55 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-55.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-55 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-56.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-56 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-56.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-56 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-56.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-56 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-57.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-57 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-57.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-57 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-58.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-58 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-58.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-58 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-58.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-58 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-59.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-59 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-59.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-59 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-60.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-60 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-60.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-60 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-60.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-60 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-61.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-61 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-61.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-61 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-61.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-61 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-62.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-62 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-62.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-62 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-62.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-62 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-63.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-63 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-63.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-63 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-64.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-64 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-64.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-64 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-64.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-64 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-65.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-65 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-65.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-65 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-65.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-65 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-66.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-66 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-66.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-66 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-66.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-66 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-67.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-67 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-67.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-67 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-67.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-67 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-68.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-68 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-68.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-68 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-69.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-69 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-69.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-69 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-69.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-69 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-70.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-70 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-70.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-70 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-71.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-71 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-71.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-71 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-71.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-71 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-72.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-72 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-72.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-72 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-72.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-72 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-73.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-73 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-73.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-73 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-73.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-73 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-74.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-74 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-74.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-74 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-75.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-75 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-75.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-75 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-75.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-75 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-76.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-76 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-76.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-76 singleton pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-76.non-core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-76 non-core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-77.core_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-77 core pangenome features
Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-77.singleton_pangenome.FeatureSet FeatureSet Ig3554_extracted_16bins.SpeciesTree.Pangenome.node-77 singleton pangenome features
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/95585
  • phylogenetic_pangenome.png
  • phylogenetic_pangenome.pdf
Compute Pangenome
Allows users to compute a pangenome from a set of individual genomes.
This app completed without errors in 1h 14m 33s.
Objects
Created Object Name Type Description
Ig3554_extracted_16bins.SpeciesTree.Pangenome Pangenome Pangenome
Summary
Pangenome saved to joval:narrative_1602053741718/Ig3554_extracted_16bins.SpeciesTree.Pangenome

13. View Function Profile

View Function Profile for a Phylogenetic Tree - v1.4.0
Examine the distribution of functional gene families for organisms in a phylogenetic SpeciesTree.
This app completed without errors in 7m 50s.
View Function Profile for a Phylogenetic Tree - v1.4.0
Examine the distribution of functional gene families for organisms in a phylogenetic SpeciesTree.
This app completed without errors in 8m 27s.
View Function Profile for a Phylogenetic Tree - v1.4.0
Examine the distribution of functional gene families for organisms in a phylogenetic SpeciesTree.
This app is new, and hasn't been started.
No output found.

14. Build Metagenome Metabolic Model

bin.013.fastaIg3554_Trimm_dastool_assembly_genome
v1 - KBaseGenomes.Genome-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/95585
Build Metagenome Metabolic Model (v0.1)
Generate a draft metabolic model based on an annotated genome.
This app completed without errors in 2h 51m 41s.
Objects
Created Object Name Type Description
Ig3554_merged_Lib_Trimm_Spades_MetaAnnotate_RAStk.metabolicmodel FBAModel FBAModel-12 Ig3554_merged_Lib_Trimm_Spades_MetaAnnotate_RAStk.metabolicmodel
Ig3554_merged_Lib_Trimm_Spades_MetaAnnotate_RAStk.metabolicmodel.gf.1 FBA FBA-13 Ig3554_merged_Lib_Trimm_Spades_MetaAnnotate_RAStk.metabolicmodel.gf.1
Report
Summary
RefGlucoseMinimal media.
Build Multiple Metabolic Models
Generate a draft metabolic model based on an annotated genome.
This app completed without errors in 7m 21s.
Objects
Created Object Name Type Description
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Unknown.fbamodel FBAModel FBAModel-12 Unknown.fbamodel
Unknown.fbamodel.gf.0 FBA FBA-13 Unknown.fbamodel.gf.0
Report
Output from Build Metagenome Metabolic Model (v0.1)
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/95585

Released Apps

  1. Annotate Metagenome Assembly with Prokka - v1.14.5
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  2. Assemble Reads with IDBA-UD - v1.1.3
    • Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28: 1420 1428. doi:10.1093/bioinformatics/bts174
  3. Assemble Reads with MEGAHIT v1.2.9
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  4. Assemble Reads with metaSPAdes - v3.13.0
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  6. 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
  7. Assess Read Quality with FastQC - v0.11.5
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  8. Build Multiple Metabolic Models
    • [1] Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Latendresse M. Efficiently gap-filling reaction networks. BMC Bioinformatics. 2014;15: 225. doi:10.1186/1471-2105-15-225
    • [4] Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM. PLOS Computational Biology. 2013;9: e1003126. doi:10.1371/journal.pcbi.1003126
    • [5] Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003;5: 264 276.
  9. Classify Taxonomy of Metagenomic Reads with GOTTCHA2 - v2.1.7
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    • GOTTCHA2 DBs from:
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  10. Classify Taxonomy of Metagenomic Reads with Kaiju - v1.7.3
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    • Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011;12: 385. doi:10.1186/1471-2105-12-385
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  11. Compare Assembled Contig Distributions - v1.1.2
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  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. Compute Pangenome
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  15. GTDB-Tk classify
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    • 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 [published online ahead of print, 2020 Apr 27]. Nat Biotechnol. 2020;10.1038/s41587-020-0501-8. DOI:10.1038/s41587-020-0501-8
    • 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
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  17. Import FASTQ/SRA File as Reads from Staging Area
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Apps in Beta

  1. Annotate and Distill Assemblies with DRAM
    • DRAM source code
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  2. Annotate Domains in a GenomeSet
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    • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10: 421. doi:10.1186/1471-2105-10-421
    • Eddy SR. Accelerated Profile HMM Searches. PLOS Computational Biology. 2011;7: e1002195. doi:10.1371/journal.pcbi.1002195
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    • Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res. 2013;41: D387 D395. doi:10.1093/nar/gks1234
    • Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res. 2018;46: D493 D496. doi:10.1093/nar/gkx922
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    • Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017;45: D200 D203. doi:10.1093/nar/gkw1129
    • Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, et al. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007;35: D260-264. doi:10.1093/nar/gkl1043
    • Tatusov RL, Koonin EV, Lipman DJ. A Genomic Perspective on Protein Families. Science. 1997;278: 631 637. doi:10.1126/science.278.5338.631
  3. Annotate Metagenome Assembly with Prokka - v1.14.5
    • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30: 2068 2069. doi:10.1093/bioinformatics/btu153
  4. 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:
  5. Build Metagenome Metabolic Model (v0.1)
    • [1] Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
  6. Build Microbial SpeciesTree - v1.6.0
    • 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
  7. Build Pangenome with OrthoMCL - v2.0
    • Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 2003;13: 2178 2189. doi:10.1101/gr.1224503
  8. Extract Bins as Assemblies - 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
  9. 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: