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SWIFT Suit
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Authors: K. Rasmussen, W. Gerlach
The SWIFT suit is a software collection for fast index-based sequence comparison.
  • SWIFT ��� fast local alignment search, guaranteeing to find epsilon-matches between two sequences.
  • SWIFT BALSAM ��� a very fast program to find semiglobal non-gapped alignments based on k-mer seeds.

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.

Users of SWIFT Suit are requested to cite :
Rasmussen, Kim R. and Stoye, Jens and Myers, Eugene W. Efficient q-gram filters for finding all epsilon-matches over a given length, JOURNAL OF COMPUTATIONAL BIOLOGY, 2006
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