BBMap pipeline

BBMap specifications

Information


Unique identifier OMICS_17796
Name BBMap
Alternative name BBTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • BBDuk
  • BBMask
  • BBMerge
  • BBNorm

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Versioning


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Maintainer


  • person_outline Brian Bushnell <>

Additional information


https://sourceforge.net/projects/bbmap/; http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2013/11/BB_User-Meeting-2014-poster-FINAL.pdf

BBMap IN pipelines

 (20)
2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] 50 bp read length, v2 chemistry) at the dna sequencing facility, department of biochemistry, university of cambridge (cambridge, uk)., raw reads from three individual samples were pre-processed using bbtools (6) and coassembled using metaspades (7). contigs were taxonomically assigned using kaiju (8) and binned on the basis of gc% and differential coverage using concoct (9)., the resulting bins we […]

2018
PMCID: 5768916
PMID: 29375529
DOI: 10.3389/fmicb.2017.02667

[…] by their common overlapping parts using pear (version 0.9.1) (zhang et al., 2014). quality metrics were checked using fastqc (version 0.11.5) and filtered using tools in fastx (version 0.7) and bbmap (version 35.84). ambiguous and chimeric sequences were identified and removed using vsearch (version 1.4.0) with the ribosomal database project as reference (rognes et al., 2016). […]

2018
PMCID: 5871332
PMID: 29582753
DOI: 10.7554/eLife.33014.035

[…] minid = 0.95 maxindel = 3 bwr = 0.16 bw = 12 quickmatch fast minhits = 2 qtrim = lr trimq = 10) and phix (parameters: k = 31 hdist = 1) sequences against the whole respective genomes using bbmap v35 (http://sourceforge.net/projects/bbmap/)., for pacbio sequencing, bsv was concentrated using precentrifugation and tff analogously to the illumina sequencing step. next, the concentrate […]

2018
PMCID: 5871332
PMID: 29582753
DOI: 10.7554/eLife.33014.035

[…] bw = 12 quickmatch fast minhits = 2 qtrim = lr trimq = 10) and phix (parameters: k = 31 hdist = 1) sequences against the whole respective genomes using bbmap v35 (http://sourceforge.net/projects/bbmap/)., for pacbio sequencing, bsv was concentrated using precentrifugation and tff analogously to the illumina sequencing step. next, the concentrate was further concentrated by sedimenting […]

2018
PMCID: 5897803
PMID: 29650582
DOI: 10.1128/genomeA.00290-18

[…] and size selected in the range of 422 to 502 bp (average size, ∼458 bp). all strains were sequenced using the illumina hiseq 4000 platform (illumina, inc., usa). sequences were trimmed using bbduk and de novo assembled using velvet 1.2.10, with the k-mer length set at 99 (22). contigs were reorganized by aligning to the genome sequence of the reference s. pseudintermedius strain 081661 […]

BBMap institution(s)
LBNL Department of Energy Joint Genome Institute, Walnut Creek, USA
BBMap funding source(s)
This work was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

BBMap review

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Zoe Jelić Matošević

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