BBMap Icon


BBMap short read aligner, and other bioinformatic tools.

Add a Review
253 Downloads (This Week)
Last Update:
Download BBMap_36.49.tar.gz
Browse All Files
Windows BSD Mac Solaris



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:


Write a Review

User Reviews

Be the first to post a review of BBMap!

Additional Project Details



Intended Audience


User Interface


Programming Language




Thanks for helping keep SourceForge clean.

Screenshot instructions:
Red Hat Linux   Ubuntu

Click URL instructions:
Right-click on ad, choose "Copy Link", then paste here →
(This may not be possible with some types of ads)

More information about our ad policies

Briefly describe the problem (required):

Upload screenshot of ad (required):
Select a file, or drag & drop file here.

Please provide the ad click URL, if possible:

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:

No, thanks