SWIFT
SWIFT is a program for fast local alignment search, guaranteeing to find epsilon-matches between two sequences. An epsilon-match is a local alignment above a given length with an error rate of at most epsilon.
SWIFT BALSAM
SWIFT BALSAM ((BAsic fiLter for Semigobal non-gapped AlignMent search) is a tool to find those reads in a set of reads (or any other DNA sequences) that have a perfect k-mer match against a given reference sequence (e.g. a genome)
Where BLAST needs a long time (hours or days) to align millions of reads against a genome, BALSAM can do this in a few minutes. It therefore can be used as a filter in a preprocessing step to find all reads with a k-mer match (and a given similarity threshold). The much smaller set of matching reads can then be "blasted" against the genome in significantly less time.
External Links
Please also take a look at RazerS. RazerS is also based on the main techniques introduced by SWIFT.
