Unknown_114
Jacqueline Rennick, Anna McLoon, Grace Zuchowski, Mishal Razi
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": "114_S46_R1_001.fastq.gz",
            "fastq_rev_staging_file_name": "114_S46_R2_001.fastq.gz",
            "name": "Unknown_114_paired_reads",
            "sequencing_tech": "Illumina",
            "single_genome": 1,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }]
    }],
    cell_id="c932a893-5314-46af-b7e7-8bef578f9438",
    run_id="cc81a904-6b24-41b8-a568-98bf072af694"
)
Assess Read Quality with FastQC - v0.11.9
A quality control application for high throughput sequence data.
This app completed without errors in 2m 52s.
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/110407
  • Unknown_114_paired_reads_110407_2_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Unknown_114_paired_reads_110407_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 14m 44s.
Objects
Created Object Name Type Description
Unknown_114_trimmed_paired PairedEndLibrary Trimmed Reads
Unknown_114_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
Unknown_114_trimmed_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 22m 57s.
Objects
Created Object Name Type Description
Unknown_114_trimmed_SPAdes.assembly Assembly Assembled contigs
Report
Summary
Assembly saved to: micronotes:narrative_1646161337815/Unknown_114_trimmed_SPAdes.assembly Assembled into 38 contigs. Avg Length: 159610.02631578947 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 37 -- 555.0 to 420360.3 bp 0 -- 420360.3 to 840165.6 bp 0 -- 840165.6 to 1259970.9 bp 0 -- 1259970.9 to 1679776.2 bp 0 -- 1679776.2 to 2099581.5 bp 0 -- 2099581.5 to 2519386.8 bp 0 -- 2519386.8 to 2939192.1 bp 0 -- 2939192.1 to 3358997.4 bp 0 -- 3358997.4 to 3778802.6999999997 bp 1 -- 3778802.6999999997 to 4198608.0 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 1h 38m 19s.
Report
Links
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 22s.
Objects
Created Object Name Type Description
Unknown_114_genomeset GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set Unknown_114_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 produced errors.
No output found.
Annotate Metagenome Assembly with Prokka - v1.14.5
Annotate Metagenome Assembly with Prokka annotation pipeline.
This app is new, and hasn't been started.
No output found.
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 5m 17s.
Objects
Created Object Name Type Description
Unknown_114_genomeprokka Genome Annotated Genome
Summary
Annotated Genome saved to: micronotes:narrative_1646161337815/Unknown_114_genomeprokka Number of genes predicted: 6305 Number of protein coding genes: 6249 Number of genes with non-hypothetical function: 3521 Number of genes with EC-number: 1370 Number of genes with Seed Subsystem Ontology: 0 Average protein length: 263 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/110407
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 15m 0s.
Objects
Created Object Name Type Description
Unknown_114_RAST Genome RAST re-annotated genome
Report
Summary
The RAST algorithm was applied to annotating a genome sequence comprised of 38 contigs containing 6065181 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, 6793 new features were called, of which 191 are non-coding. Output genome has the following feature types: Coding gene 6602 Non-coding prophage 3 Non-coding repeat 129 Non-coding rna 59 Overall, the genes have 3396 distinct functions The genes include 2557 genes with a SEED annotation ontology across 1475 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. 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
  5. 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.
  6. Assess Read Quality with FastQC - v0.11.9
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  7. 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
  8. 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
  9. 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