BFAST (Blat-like Fast Accurate Search Tool) 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.
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Homer N, Merriman B, Nelson SF.
BFAST: An alignment tool for large scale genome resequencing.
PLoS ONE. 2009 4(11): e7767.