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Attention:
Due to technical maintenance some tools might be unavailable. See maintenance information. 
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SWIFT Suit
The SWIFT suit is a software collection for fast index-based
sequence comparison. It contains the following
programs:
- 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.
All tools can be dowloaded from the download section on the right side.
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.
K. R. Rasmussen, J. Stoye and G. Myers.
Efficient q-Gram Filters for Finding All epsilon-Matches
over a Given Length
In Proc. of the 9th Conf. on Computational Molecular Biology
(RECOMB'05), Cambridge, MA, 2005. (preprint)
K. Rasmussen, J. Stoye, E. W. Myers
Efficient q-Gram Filters for Finding All epsilon-Matches
over a Given Length
In J. Comp. Biol. 13(2), 296-308, 2006.
SWIFT BALSAM (BAsic fiLter for Semigobal non-gapped AlignMent search)
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.
If you need another output format, please contact the author.
The author Wolfgang Gerlach and the url http://bibiserv.techfak.uni-bielefeld.de/swift/
External Links
Please take a look at RazerS. RazerS is also based on the main techniques introduced by SWIFT.
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