OnWorks favicon

BBMap download for Windows

Free download BBMap Windows app to run online win Wine in Ubuntu online, Fedora online or Debian online

This is the Windows app named BBMap whose latest release can be downloaded as BBMap_38.95.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.

Download and run online this app named BBMap with OnWorks for free.

Follow these instructions in order to run this app:

- 1. Downloaded this application in your PC.

- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 3. Upload this application in such filemanager.

- 4. Start any OS OnWorks online emulator from this website, but better Windows online emulator.

- 5. From the OnWorks Windows OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 6. Download the application and install it.

- 7. Download Wine from your Linux distributions software repositories. Once installed, you can then double-click the app to run them with Wine. You can also try PlayOnLinux, a fancy interface over Wine that will help you install popular Windows programs and games.

Wine is a way to run Windows software on Linux, but with no Windows required. Wine is an open-source Windows compatibility layer that can run Windows programs directly on any Linux desktop. Essentially, Wine is trying to re-implement enough of Windows from scratch so that it can run all those Windows applications without actually needing Windows.





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!


  • 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: bbmap.sh 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: http://seqanswers.com/forums/showthread.php?t=58221



User interface


Programming Language



Bio-Informatics, Medical Science Apps.

This is an application that can also be fetched from https://sourceforge.net/projects/bbmap/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.