Draft Genome Assembly Bacillus Subtilis
Diego A. Esquivel-Hernández, ADRIANA LIZETH CASANOVA OLGUIN
Generated February 22, 2024
Assess Read Quality with FastQC - v0.12.1
A quality control application for high throughput sequence data.
This app completed without errors in 51s.
Report
Links
  • index.html - HTML files generated by fastqc that contains report on quality of reads
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/171478
  • Bsubtilis_rawdata_171478_2_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Bsubtilis_rawdata_171478_2_1.fwd_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 1m 57s.
Objects
Created Object Name Type Description
B_subtilis_trimmed_paired PairedEndLibrary Trimmed Reads
B_subtilis_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
B_subtilis_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Report
Links
Assess Read Quality with FastQC - v0.12.1
A quality control application for high throughput sequence data.
This app completed without errors in 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/171478
  • B_subtilis_trimmed_paired_171478_4_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • B_subtilis_trimmed_paired_171478_4_1.fwd_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 3m 12s.
Objects
Created Object Name Type Description
SPAdes.Assembly_b_subtilis_hort Assembly Assembled contigs
Report
Summary
Assembly saved to: diegoibt:narrative_1708458907164/SPAdes.Assembly_b_subtilis_hort Assembled into 40 contigs. Avg Length: 102520.25 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 34 -- 506.0 to 103305.2 bp 0 -- 103305.2 to 206104.4 bp 3 -- 206104.4 to 308903.6 bp 0 -- 308903.6 to 411702.8 bp 0 -- 411702.8 to 514502.0 bp 0 -- 514502.0 to 617301.2 bp 0 -- 617301.2 to 720100.4 bp 0 -- 720100.4 to 822899.6 bp 0 -- 822899.6 to 925698.7999999999 bp 3 -- 925698.7999999999 to 1028498.0 bp
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 2m 16s.
Objects
Created Object Name Type Description
Spades.Assembly_B_subtilis_hort_prokka Genome Annotated Genome
Summary
Annotated Genome saved to: diegoibt:narrative_1708458907164/Spades.Assembly_B_subtilis_hort_prokka Number of genes predicted: 4155 Number of protein coding genes: 4099 Number of genes with non-hypothetical function: 2870 Number of genes with EC-number: 1034 Number of genes with Seed Subsystem Ontology: 0 Average protein length: 292 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/171478
Annotate Microbial Assembly with RASTtk - v1.073
Annotate a bacterial or archaeal assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 4m 14s.
Objects
Created Object Name Type Description
Spades_assembly_b_subtilis_hort_rast Genome RAST annotation
Summary 
The RAST algorithm was applied to annotating a genome sequence comprised of 40 contigs containing 4100810 nucleotides. 
No initial gene calls were provided.
Standard features were called using: glimmer3; prodigal.
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, 4403 new features were called, of which 83 are non-coding.
Output genome has the following feature types:
	Coding gene                     4320 
	Non-coding repeat                 28 
	Non-coding rna                    55 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
Output from Annotate Microbial Assembly with RASTtk - v1.073
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/171478
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 5m 46s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/171478
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Circular Genome Visualization Tool
Generate a map and annotations of circular genomes using CGView.
This app completed without errors in 52s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/171478
  • KBase_derived_Spades.Assembly_B_subtilis_hort_prokka.png
  • KBase_derived_Spades.Assembly_B_subtilis_hort_prokka.jpg
  • KBase_derived_Spades.Assembly_B_subtilis_hort_prokka.svg
Circular Genome Visualization Tool
Generate a map and annotations of circular genomes using CGView.
This app completed without errors in 1m 24s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/171478
  • KBase_derived_Spades_assembly_b_subtilis_hort_rast.png
  • KBase_derived_Spades_assembly_b_subtilis_hort_rast.jpg
  • KBase_derived_Spades_assembly_b_subtilis_hort_rast.svg
Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 3m 37s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/171478
  • Tree_b_subtilis_hort.newick
  • Tree_b_subtilis_hort-labels.newick
  • Tree_b_subtilis_hort.png
  • Tree_b_subtilis_hort.pdf
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 3s.
Objects
Created Object Name Type Description
Spades_assembly_b_subtilis_hort_rast Genome Taxonomy and taxon_assignment updated with GTDB
Report
Links

Released Apps

  1. 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
  2. Annotate Microbial 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.vThe 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
  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 Genome Quality with CheckM - v1.0.18
    • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114
    • CheckM source:
    • Additional info:
  5. Assess Read Quality with FastQC - v0.12.1
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  6. Circular Genome Visualization Tool
    no citations
  7. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  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

Apps in Beta

  1. 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