BFAST: Blat-like Fast Accurate Search Tool
Welcome to the home page for BFAST. BFAST stand 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 https://sourceforge.net/projects/bfast/files/. Alternatively, see our project page at: https://sourceforge.net/projects/bfast/. 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".
Please cite the website "http://genome.ucla.edu/bfast" 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
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 anthing else. Click here to subscribe
firstname.lastname@example.org The Developer's voice: discussion on development (for developers). Click here to subscribe
Join the bfast channel at freenode if you want to discuss about BFAST over IRC.
Network: freenode, name: #bfast, url: irc://freenode/bfast.
The BFAST Book
The BFAST book is available in the "manual" directory in the specific bfast release.
Simulated datasets that accompany the BFAST paper can be found at bfast.paper.simulations.04.tar.bz2.
The example dataset for Phi X 174 in the bfast book can be found at bfast-example-phi.x.174.tar.gz.
Please contact Nils Homer (email@example.com) with any questions or concerns. For general help, please use the mailing lists.
This research was partially supported by University of California Systemwide Biotechnology Research and Education Program GREAT Training Grant 2007-10 (to NH), the NIH Neuroscience Microarray Consortium (U24NS052108), and a grant from the NIMH (R01 MH071852). We would also like to thank Jim Kent for creating and distributing the BLAT program, which was both a motivation for this work, and was also the basis for our practical large scale alignment pipeline for the past 18 months. We also thank members of the Nelson Lab: Zugen Chen, Hane Lee, Bret Harry, Jordan Mendler, Brian O'Connor for input and computational infrastructure support.