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BFAST is a universal DNA sequence aligner tool developed at UCLA by Nils Homer.

The BFAST Web Server is a user-friendly way to quickly align short reads to reference sequences in both nucleotide space as well as ABI SOLiD color space.

Utilities include BFAST alignment, conversion between nucleotide and color space, calculating the a priori power of the alignments, as well as a utility to perform smith-waterman local alignment.


  • Explicit time and accuracy tradeoff with a prior accuracy estimation, supported by indexing the reference sequences. Optimally compresses indexes.
  • Can handle billions of short reads.
  • Can handle DNA insertions, DNA deletions, SNPs, and color errors (can map ABI SOLiD color space reads).
  • Performs a full Smith Waterman alignment.

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