BFAST: Blat-like Fast Accurate Search Tool
Welcome to the home page for BFAST. BFAST stands for the "Blat-like Fast Accurate Search Tool".
BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include:
- Speed: enables billions of short reads to be mapped quickly.
- Accuracy: A priori probabilities for mapping reads with defined set of variants.
- An easy way to measurably tune accuracy at the expense of speed.
Specifically, BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance.
BFAST supports both Illumina and ABI SOLiD data, as well as any other Next-Generation Sequencing Technology (454, Helicos), with particular emphasis on sensitivity towards errors, SNPs and especially indels. Other algorithms take short-cuts by ignoring errors, certain types of variants (indels), and even require further alignment, all to be the "fastest" (but still not complete). BFAST is able to be tuned to find variants regardless of the error-rate, polymorphism rate, or other factors.
Get it Now
To get BFAST now, see http://sourceforge.net/projects/bfast/files/. You can get the latest BFAST by using GIT: "git clone git://bfast.git.sourceforge.net/gitroot/bfast/bfast". You can get the latest BFAST Server by using GIT: "git clone git://bfast.git.sourceforge.net/gitroot/bfast/bfast-server".
We also have a version that incorporates some elements of BWA. This may be useful when aligning short reads, or for paired-end SOLiD data. Please see the bfast+bwa release, or the bfast+bwa branch within the repository.
There are three mailing lists:
firstname.lastname@example.org The voice of BFAST: announcement of releases and critical bug fixes. Click here to subscribe
email@example.com The User's voice: bug report, feature request, troubleshooting and anything else. Click here to subscribe
firstname.lastname@example.org The Developer's voice: discussion on development (for developers). Click here to subscribe
A great forum exists at SeqAnswers.com.
Join the bfast channel at freenode if you want to discuss about BFAST over IRC.
Network: freenode, name: #bfast, url: irc://freenode/bfast.
For frequently asked questions, see our FAQ
Please cite the website "http://bfast.sourceforge.net" as well as the accompanying papers: Homer N, Merriman B, Nelson SF. BFAST: An alignment tool for large scale genome resequencing. PMID: 19907642 PLoS ONE. 2009 4(11): e7767. http://dx.doi.org/10.1371/journal.pone.0007767 Homer N, Merriman B, Nelson SF. Local alignment of two-base encoded DNA sequence. BMC Bioinformatics. 2009 Jun 9;10(1):175. PMID: 19508732 http://dx.doi.org/10.1186/1471-2105-10-175
Please contact Nils Homer (email@example.com) with any questions or concerns. For general help, please use the mailing lists.