JC28-genome
Andrea Suria
Generated August 18, 2020

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from biokbase.narrative.jobs.jobmanager import JobManager
JobManager().get_job('5936c44be4b0b89082da637f')
Out[ ]:
FastQC - read quality analysis
A quality control application for high throughput sequence data.
This app completed without errors in 8m 56s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/21814
  • ffd705fc-85ce-4dd9-a44f-99b8bee62cbc.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • bcd70199-be58-4b44-8308-1bf478f3b8f4.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Trimmomatic - Read Trimming
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 22m 3s.
Objects
Created Object Name Type Description
JC28-genome-reads-trimmed_paired PairedEndLibrary Trimmed Reads
JC28-genome-reads-trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
JC28-genome-reads-trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Report
Assess Read Quality with FastQC - v0.11.5
A quality control application for high throughput sequence data.
This app produced errors.
No output found.
Assemble with A5
Assemble paired-end microbial reads using the A5 assembly pipeline.
This app completed without errors in 2h 58m 45s.
Objects
Created Object Name Type Description
JC28-genome-a5.contigs Assembly Assembled contigs
Summary
============= Raw Contigs ============ QUAST: All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). Assembly a5_contigs # contigs (>= 0 bp) 40 # contigs (>= 1000 bp) 31 Total length (>= 0 bp) 5533243 Total length (>= 1000 bp) 5527245 # contigs 39 Largest contig 1226393 Total length 5532803 GC (%) 43.19 N50 509001 N75 314808 L50 4 L75 8 # N's per 100 kbp 3.16 ========== Filtered Contigs ========== ContigSet saved to: asuria25:narrative_1496760868085/JC28-genome-a5.contigs Assembled into 40 contigs. Average Length: 138331.075 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 29 -- 440.0 to 123035.3 bp 2 -- 123035.3 to 245630.6 bp 2 -- 245630.6 to 368225.9 bp 3 -- 368225.9 to 490821.2 bp 3 -- 490821.2 to 613416.5 bp 0 -- 613416.5 to 736011.8 bp 0 -- 736011.8 to 858607.1 bp 0 -- 858607.1 to 981202.4 bp 0 -- 981202.4 to 1103797.7 bp 1 -- 1103797.7 to 1226393.0 bp
Output from Assemble with A5
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/21814
Assemble with Velvet
Assemble short microbial reads using the Velvet assembler.
This app completed without errors in 5m 50s.
Objects
Created Object Name Type Description
JC28-genome-velvet.contigs Assembly Assembled contigs
Summary
============= Raw Contigs ============ QUAST: All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). Assembly velvet_contigs # contigs (>= 0 bp) 592 # contigs (>= 1000 bp) 120 Total length (>= 0 bp) 5461918 Total length (>= 1000 bp) 5395649 # contigs 143 Largest contig 230148 Total length 5410830 GC (%) 43.21 N50 98222 N75 59709 L50 18 L75 37 # N's per 100 kbp 126.15 ========== Filtered Contigs ========== ContigSet saved to: asuria25:narrative_1496760868085/JC28-genome-velvet.contigs Assembled into 169 contigs. Average Length: 32076.1597633 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 110 -- 307.0 to 23291.1 bp 13 -- 23291.1 to 46275.2 bp 20 -- 46275.2 to 69259.3 bp 5 -- 69259.3 to 92243.4 bp 6 -- 92243.4 to 115227.5 bp 5 -- 115227.5 to 138211.6 bp 4 -- 138211.6 to 161195.7 bp 2 -- 161195.7 to 184179.8 bp 1 -- 184179.8 to 207163.9 bp 3 -- 207163.9 to 230148.0 bp
Output from Assemble with Velvet
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/21814
Assess Quality of Assemblies with QUAST - v4.4
Run QUAST (QUality ASsessment Tool) on a set of Assemblies to assess their quality.
This app is still in progress.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 32m 49s.
No output found.
Assess Genome Quality with CheckM - v1.0.8
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies
This app completed without errors in 8m 36s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/21814
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM

Apps

  1. Align Reads using Bowtie2 - v2.3.2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9: 357 359. doi:10.1038/nmeth.1923
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi:10.1186/gb-2009-10-3-r25
  2. Assemble with A5
    • Coil, D., Jospin, G. and Darling, A.E., (2014). A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics, p.btu661.
  3. Assemble with Velvet
    • Zerbino, D. R., Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18(5), 821-829, doi: 10.1101/gr.074492.107
  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 Quality of Assemblies with QUAST - v4.4
    • [1] Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29: 1072 1075. doi:10.1093/bioinformatics/btt086
    • [2] Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A. Icarus: visualizer for de novo assembly evaluation. Bioinformatics. 2016;32: 3321 3323. doi:10.1093/bioinformatics/btw379
  6. Assess Read Quality with FastQC - v0.11.5
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  7. 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