Project Description
A group of tools run on Windows for Bioinformatics. Include ported tools from Linux (e.g. BWA, SAMTOOLS), and later original Windows applications.

What's NEW:

Project Fourtytwo released for preview. or This is BOW's first original work. Together with tools already here you can have your own NGS pipeline on Windows Azure. It has been internally tested for a while on human sequence data. We also did a demo of the running system at Microsoft eScience Workshop 2012 in Chicago. Check it out!

Tools can't live without.


Tabix - Generic indexer for TAB-delimited genome position files, is up for download. This is a response to a discussion here TABIX.

Code on GitHub:

samtools updated with bug fix, please download the new release.


BWA with multi-threading SAMPE is up for download, please make sure you read the release page: BWA (Burrows-Wheeler Aligner) Multi-thread SAMPE

The code is up to GitHub:


samtools updated with bug fix, please download and use this new release. Read the details on release page: samtools (Tools for alignments in the SAM format)


Usage notes: New Line on Windows and Linux.


samtools up for download, the source code is here:

Please make sure you read the release notes here:

Since Codeplex doesn't support GPLv3, now the BWA source code is up here:

Short survey: if you don't mind telling me your affiliation and a paragraph about why you plan to run these tools on Windows, or some suggestions to the next tool I should work on, either via Codeplex or Github, or email, I would be very thankful! :)

BWA is up for download, SAMTOOLS will be up very soon. Keep checking.

Last edited Feb 19, 2013 at 11:43 AM by xied75, version 15