Unknown_111
Abigail Kirsty Sheridan, Katie Touchette, Rebecca Draper
Generated August 23, 2022
# Welcome to the Narrative
from IPython.display import IFrame
IFrame("https://www.kbase.us/narrative-welcome-cell/", width="100%", height="300px")
Out[1]:
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_bulk(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "31e93066beb421a51b9c8e44b1201aa93aea0b4e",
        "params": [{
            "fastq_fwd_staging_file_name": "111_S44_R1_001.fastq (1).gz",
            "fastq_rev_staging_file_name": "111_S44_R2_001.fastq.gz",
            "name": "Unknown111pairedreads",
            "sequencing_tech": "Illumina",
            "single_genome": 1,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }]
    }],
    cell_id="d527449f-2ae7-470a-960a-6542ddf8f417",
    run_id="592b540b-d1dc-4426-aac9-5e918a3dd0bd"
)
Assess Read Quality with FastQC - v0.11.9
A quality control application for high throughput sequence data.
This app completed without errors in 3m 26s.
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/110406
  • Unknown111pairedreads_110406_2_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Unknown111pairedreads_110406_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 13m 49s.
Objects
Created Object Name Type Description
Unknown_111_Trimmedreads_paired PairedEndLibrary Trimmed Reads
Unknown_111_Trimmedreads_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
Unknown_111_Trimmedreads_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Report
Links
Assemble Reads with SPAdes - v3.15.3
Assemble reads using the SPAdes assembler.
This app completed without errors in 19m 49s.
Objects
Created Object Name Type Description
Unknown11_SPAdes.Assembly Assembly Assembled contigs
Report
Summary
Assembly saved to: ak28sher:narrative_1646161334372/Unknown11_SPAdes.Assembly Assembled into 36 contigs. Avg Length: 121709.05555555556 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 9 -- 602.0 to 38461.3 bp 9 -- 38461.3 to 76320.6 bp 5 -- 76320.6 to 114179.90000000001 bp 1 -- 114179.90000000001 to 152039.2 bp 2 -- 152039.2 to 189898.5 bp 3 -- 189898.5 to 227757.80000000002 bp 1 -- 227757.80000000002 to 265617.10000000003 bp 2 -- 265617.10000000003 to 303476.4 bp 2 -- 303476.4 to 341335.7 bp 2 -- 341335.7 to 379195.0 bp
Links
Classify Microbes with GTDB-Tk - v1.7.0
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 34m 2s.
Report
Links
Unknown11_SPAdes.Assembly
v1 - KBaseGenomeAnnotations.Assembly-5.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/110406
Unknown11_SPAdes.Assembly
v1 - KBaseGenomeAnnotations.Assembly-5.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/110406
Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
Annotate Assembly and Re-annotate Genomes with Prokka annotation pipeline.
This app completed without errors in 4m 11s.
Objects
Created Object Name Type Description
Unknown_111_annotated_prokka Genome Annotated Genome
Summary
Annotated Genome saved to: ak28sher:narrative_1646161334372/Unknown_111_annotated_prokka Number of genes predicted: 4503 Number of protein coding genes: 4463 Number of genes with non-hypothetical function: 2522 Number of genes with EC-number: 1018 Number of genes with Seed Subsystem Ontology: 0 Average protein length: 278 aa.
Unknown_111_annotated_prokka
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/110406
Output from Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/110406
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 35s.
Objects
Created Object Name Type Description
unknown_111_Genomeset GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set unknown_111_Genomeset: 1
Annotate and Distill Genomes with DRAM
Annotate your genome(s) with DRAM. Annotations will then be distilled to create an interactive functional summary per genome.
This app completed without errors in 36m 22s.
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/110406
  • annotations.tsv - DRAM annotations in a tab separate table format
  • genes.faa - Genes as amino acids predicted by DRAM with brief annotations
  • product.tsv - DRAM product in tabular format
  • metabolism_summary.xlsx - DRAM metabolism summary tables
  • genome_stats.tsv - DRAM genome statistics table
Build Metabolic Model
Construct a draft metabolic model based on an annotated genome.
This app completed without errors in 2m 7s.
Objects
Created Object Name Type Description
unknown_111_metabolicmodel FBAModel FBAModel-14 unknown_111_metabolicmodel
unknown_111_metabolicmodel.gf.1 FBA FBA-13 unknown_111_metabolicmodel.gf.1
Report
Summary
RefGlucoseMinimal media.
Output from Build Metabolic Model
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/110406

Apps

  1. Annotate and Distill Genomes with DRAM
    • DRAM source code
    • DRAM documentation
    • DRAM publication
  2. Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
    • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30: 2068 2069. doi:10.1093/bioinformatics/btu153
  3. Assemble Reads with SPAdes - v3.15.3
    • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology. 2012;19: 455-477. doi: 10.1089/cmb.2012.0021
    • Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102.
  4. Assess Read Quality with FastQC - v0.11.9
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  5. Build GenomeSet - v1.7.6
    • 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
  6. Build Metabolic Model
    • [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.
  7. Classify Microbes with GTDB-Tk - v1.7.0
    • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks, GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, Volume 36, Issue 6, 15 March 2020, Pages 1925 1927. DOI: https://doi.org/10.1093/bioinformatics/btz848
    • Parks, D., Chuvochina, M., Waite, D. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36, 996 1004 (2018). DOI: https://doi.org/10.1038/nbt.4229
    • Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;10.1038/s41587-020-0501-8. DOI:10.1038/s41587-020-0501-8
    • Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Dav n AA, Waite DW, Whitman WB, Parks DH, and Hugenholtz P. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol. 2021 Jul;6(7):946-959. DOI:10.1038/s41564-021-00918-8
    • 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
  8. Trim Reads with Trimmomatic - v0.36
    • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114 2120. doi:10.1093/bioinformatics/btu170