Unknown_107
Kaitlyn Devine, Anna McLoon, Molly Bogardus, Thomas Awad
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]:
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 11m 21s.
Objects
Created Object Name Type Description
Unknown_107_trimmed_paired PairedEndLibrary Trimmed Reads
Unknown_107_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
Unknown_107_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Report
Links 
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": "107_S43_R1_001.fastq (3).gz",
            "fastq_rev_staging_file_name": "107_S43_R2_001.fastq.gz",
            "name": "Unknown_107_paired_reads",
            "sequencing_tech": "Illumina",
            "single_genome": 1,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }]
    }],
    cell_id="8279841f-1cf5-4a99-a40b-d5386285ee9e",
    run_id="5b23afb9-a294-431f-9953-4beb58b5512a"
)
Assess Read Quality with FastQC - v0.11.9
A quality control application for high throughput sequence data.
This app completed without errors in 2m 50s.
Report
Links
  • index.html - HTML files generated by fastqc that contains report on quality of reads
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/110380
  • Unknown_107_paired_reads_110380_2_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Unknown_107_paired_reads_110380_2_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Assemble Reads with SPAdes - v3.15.3
Assemble reads using the SPAdes assembler.
This app completed without errors in 17m 13s.
Objects
Created Object Name Type Description
Unknown_107_trimmed_SPAdes.Assembly Assembly Assembled contigs
Report
Summary
Assembly saved to: ka24devi:narrative_1646143271343/Unknown_107_trimmed_SPAdes.Assembly Assembled into 97 contigs. Avg Length: 58910.21649484536 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 79 -- 510.0 to 70433.7 bp 4 -- 70433.7 to 140357.4 bp 5 -- 140357.4 to 210281.09999999998 bp 3 -- 210281.09999999998 to 280204.8 bp 2 -- 280204.8 to 350128.5 bp 0 -- 350128.5 to 420052.19999999995 bp 2 -- 420052.19999999995 to 489975.89999999997 bp 1 -- 489975.89999999997 to 559899.6 bp 0 -- 559899.6 to 629823.2999999999 bp 1 -- 629823.2999999999 to 699747.0 bp
Links
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 46s.
Objects
Created Object Name Type Description
Unknown_107_build_genome_set GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set Unknown_107_build_genome_set: 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 41m 16s.
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/110380
  • 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
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 38m 55s.
Report
Links
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 7m 6s.
Objects
Created Object Name Type Description
unknown_107_annotation Genome Annotated Genome
Summary
Annotated Genome saved to: ka24devi:narrative_1646143271343/unknown_107_annotation Number of genes predicted: 5885 Number of protein coding genes: 5839 Number of genes with non-hypothetical function: 2997 Number of genes with EC-number: 1136 Number of genes with Seed Subsystem Ontology: 0 Average protein length: 259 aa.
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/110380
Annotate Genome/Assembly with RASTtk - v1.073
Annotate or re-annotate genome/assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 12m 49s.
Objects
Created Object Name Type Description
unknown_107_RAST Genome RAST re-annotated genome
Report
Summary
The RAST algorithm was applied to annotating a genome sequence comprised of 97 contigs containing 5714291 nucleotides. No initial gene calls were provided. Standard gene features were called using: prodigal; glimmer3. A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr. The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity. In addition to the remaining original 0 coding features and 0 non-coding features, 6640 new features were called, of which 388 are non-coding. Output genome has the following feature types: Coding gene 6252 Non-coding crispr_array 1 Non-coding crispr_repeat 28 Non-coding crispr_spacer 27 Non-coding prophage 2 Non-coding repeat 287 Non-coding rna 43 Overall, the genes have 3784 distinct functions The genes include 1862 genes with a SEED annotation ontology across 1373 distinct SEED functions. The number of distinct functions can exceed the number of genes because some genes have multiple functions.
Links

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. Annotate Genome/Assembly with RASTtk - v1.073
    • [1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • [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] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365
    • [4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202
    • [5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389
    • [6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964.
    • [7] Cobucci-Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16: 793 803. doi:10.1007/s00792-012-0482-8
    • [8] Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009;37 6643-54. doi:10.1093/nar/gkp698.
    • [9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179.
    • [10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120
    • [11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • [12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009
    • [13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406
  4. 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.
  5. Assess Read Quality with FastQC - v0.11.9
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  6. 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
  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