BBMap short read aligner, and other bioinformatic tools.

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This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.

BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast.

BBNorm: Kmer-based error-correction and normalization tool.

Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity.

Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s.

BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file.

...and more!

BBMap Web Site


  • Pure Java, runs on any platform; already compiled, just unzip and run.
  • Fast, efficient, and multithreaded.
  • Usage information displayed when running a shellscript with no parameters.
  • Highest sensitivity of any short-read aligner.
  • Easy to install - just unzip/untar.
  • Easy to use. Example: ref=ecoli.fa in=reads.fq out=mapped.sam
  • Handles all common formats: fasta, fastq, sam, scarf, fasta+qual, ASCII-33, ASCII-64, gzip.
  • Used by the Joint Genome Institute.
  • BB stands for Bestus Bioinformaticus.
  • There is a handy FAQ here:


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