Welcome to the home page for BFAST on Solid Software Tools. BFAST stand for the "Blat-like Fast Accurate Search Tool".

We have moved!  Find us at bfast.sourceforge.net.

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 is able to map in both color space and nucleotide space.  It uses a full local Smith-Waterman algorithm to score alignment, correcting for color errors, allowing for mutations/variants/SNPs, insertions, and deletions.

Please cite the website "http://genome.ucla.edu/bfast" as well as the accompanying 
paper (Nils Homer, Stanley F. Nelson and Barry Merriman. 2009 (Unpublished)).