BBMap specifications


Unique identifier OMICS_17796
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


  • BBDuk
  • BBMask
  • BBMerge
  • BBNorm



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  • person_outline Brian Bushnell <>

Additional information;

BBMap citations

PMCID: 5947290

[…] was assessed using fastqc and reads were processed, including adapter clipping, trimming of their 5′ and 3′ ends (5–10 bases) and removal of reads with quality < 10 and length < 25 bp using bbduk (v35.14). reads from each aom enrichment library were mapped to the respective draft genomes with a minimum identity threshold of 98%. reads that were unambiguously mapped to a gene […]

PMCID: 5527411

[…] was performed using a 600-cycle miseq reagent kit (version 3), and samples were sequenced in batches of between 1 and 13 on a single flow cell., raw sequencing reads were adapter trimmed using bbduk ( and the adapter sequence file provided within the bbmap package; the following parameters were used: minlength, 36; k,19; ktrim, r; hdist, 1; mink, 12. […]

PMCID: 5493772

[…] run mode, generating paired or single-end 100 bp reads., for the bar-seq libraries sequenced with a paired-read protocol, the read mates were merged into single reads using bbmerge v. 8.82 from the bbtools/bbmap analysis suite ( following that preliminary step, the same analysis procedure was then used on the reads originating from all the libraries, […]

PMCID: 5118689

[…] of the purity parameter was conducted inside the r statistical package18 (fig. 3) with bioconductor shortread package with critical components implemented from stand-alone software projects such as bbmap19, starcode15 and bowtie220 (see materials and methods for details or the full git repository at, the barcode structure in this experiment […]

PMCID: 5073256

[…] for 2 weeks, after which total dna was isolated and sequenced using the illumina hiseq 2000 platform as previously described (7). adaptor and bar code sequences were removed from all reads using bbduk of the bbtool packages (, and the reads were de novo assembled into scaffolds using clc genomics workbench v8 with default settings. […]

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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BBtoolkit has almost everything you ever need, so many different tools

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