Arthrobacter_ATCC_49987
Nidhi
Generated June 19, 2020
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app completed without errors in 7m 16s.
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/64079
  • Arthrobacteria_S3_L001_R1_001.fastq_64079_2_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • Arthrobacteria_S3_L001_R1_001.fastq_64079_2_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
MaSuRCA Assembler - v3.2.9
Assemble reads using the MaSuRCA assembler.
This app completed without errors in 2h 54m 47s.
Objects
Created Object Name Type Description
masurca.contigs Assembly Assembled contigs
Report
Summary
MaSuRCA results saved to: nidhi112000:narrative_1591651461207//kb/module/work/tmp/507f04d7-56db-44e4-9b8b-1bd4d458397a/masurca_project_dir/CA.mr.41.15.15.0.02 Assembly saved to: nidhi112000:narrative_1591651461207/masurca.contigs Assembled into 3 contigs. Avg Length: 1467446.33333 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 2 -- 65535.0 to 475953.6 bp 0 -- 475953.6 to 886372.2 bp 0 -- 886372.2 to 1296790.8 bp 0 -- 1296790.8 to 1707209.4 bp 0 -- 1707209.4 to 2117628.0 bp 0 -- 2117628.0 to 2528046.6 bp 0 -- 2528046.6 to 2938465.2 bp 0 -- 2938465.2 to 3348883.8 bp 0 -- 3348883.8 to 3759302.4 bp 1 -- 3759302.4 to 4169721.0 bp
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/64079
  • masurca_output.zip - Output file(s) generated by MaSuRCA
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 7m 50s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/64079
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Annotate Assembly and Re-annotate Genomes with Prokka(v1.12)
Annotate Assembly and Re-annotate Genomes with Prokka annotation pipeline.
This app completed without errors in 3m 44s.
Objects
Created Object Name Type Description
Arthrobacter_ATCC_49987 Genome Annotated Genome
Summary
Annotated Genome saved to: nidhi112000:narrative_1591651461207/Arthrobacter_ATCC_49987 Number of genes predicted: 4129 Number of protein coding genes: 4053 Number of genes with non-hypothetical function: 2471 Number of genes with EC-number: 1440 Number of genes with Seed Subsystem Ontology: 1155 Average protein length: 317 aa.
Output from Annotate Assembly and Re-annotate Genomes with Prokka(v1.12)
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/64079
Build GenomeSet - v1.0.1
Allows users to create a GenomeSet object.
This app completed without errors in 2m 12s.
Objects
Created Object Name Type Description
Arthrobacter_GenomeSet GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set Arthrobacter_GenomeSet: 31
Output from Build GenomeSet - v1.0.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/64079
Insert Set of Genomes Into SpeciesTree - v2.2.0
Add a user-provided GenomeSet to a KBase SpeciesTree.
This app completed without errors in 10m 20s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/64079
  • Arthrobacter_Tree.newick
  • Arthrobacter_Tree-labels.newick
  • Arthrobacter_Tree.png
  • Arthrobacter_Tree.pdf

Apps

  1. Annotate Assembly and Re-annotate Genomes with Prokka(v1.12)
    • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30: 2068 2069. doi:10.1093/bioinformatics/btu153
  2. 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:
  3. Assess Read Quality with FastQC - v0.11.5
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  4. Build GenomeSet - v1.0.1
    • 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
  5. Insert Set of Genomes 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
  6. MaSuRCA Assembler - v3.2.9
    • Zimin AV, Mar ais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29: 2669 2677. doi:10.1093/bioinformatics/btt476