M.luteus_ATCC_ 49442
Nidhi
Generated April 29, 2020
MaSuRCA Assembler - v3.2.9
MaSuRCA consists of three main steps:1.Create config.txt file 2.Generate assemble.sh 3.Assemble reads
This app completed without errors in 2h 21m 19s.
Objects
Created Object Name Type Description
MLuteus_masurca.contigs Assembly Assembled contigs
Report
Summary
MaSuRCA results saved to: nidhi112000:narrative_1575664719674//kb/module/work/tmp/7fa2fc4e-aa9a-4b5b-86da-2ba9f83bba19/masurca_project_dir/CA.mr.41.15.15.0.02 Assembly saved to: nidhi112000:narrative_1575664719674/MLuteus_masurca.contigs Assembled into 2 contigs. Avg Length: 2494570.5 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1 -- 235336.0 to 687182.9 bp 0 -- 687182.9 to 1139029.8 bp 0 -- 1139029.8 to 1590876.7 bp 0 -- 1590876.7 to 2042723.6 bp 0 -- 2042723.6 to 2494570.5 bp 0 -- 2494570.5 to 2946417.4 bp 0 -- 2946417.4 to 3398264.3 bp 0 -- 3398264.3 to 3850111.2 bp 0 -- 3850111.2 to 4301958.1 bp 1 -- 4301958.1 to 4753805.0 bp
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/58065
  • masurca_output.zip - Output file(s) generated by MaSuRCA
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 5m 16s.
Objects
Created Object Name Type Description
MLuteus_masurca_RAST Genome Annotated genome
Summary 
The RAST algorithm was applied to annotating a genome sequence comprised of 2 contigs containing 4989141 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, 4883 new features were called, of which 181 are non-coding.
Output genome has the following feature types:
	Coding gene                     4702 
	Non-coding repeat                116 
	Non-coding rna                    65 
Overall, the genes have 2350 distinct functions. 
The genes include 2224 genes with a SEED annotation ontology across 1079 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
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/58065
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 45s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/58065
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Build GenomeSet - v1.0.1
Allows users to create a GenomeSet object.
This app completed without errors in 2m 27s.
Objects
Created Object Name Type Description
GenomeSet_ATCC_49442 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set GenomeSet_ATCC_49442: 35
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/58065
Insert Set of Genomes Into Species Tree 2.1.10
Add a user-provided GenomeSet to a KBase species tree.
This app completed without errors in 52m 6s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/58065
  • ATCC_49442_Tree.newick
  • ATCC_49442_Tree-labels.newick
  • ATCC_49442_Tree.png
  • ATCC_49442_Tree.pdf

Apps

  1. Annotate Microbial Assembly
    • 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
    • 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: 8365. doi:10.1038/srep08365
    • 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: D206-214. doi:10.1093/nar/gkt1226
  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. 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
  4. Insert Set of Genomes Into Species Tree 2.1.10
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010 Mar 10;5(3):e9490
  5. 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