PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of “seed” words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.
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Bioinformatics. 2013 Jan 15;29(2):268-70. doi: 10.1093/bioinformatics/bts675. Epub 2012 Nov 17.
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Campagna D1, Telatin A, Forcato C, Vitulo N, Valle G.
Bioinformatics. 2009 Apr 1;25(7):967-8. Epub 2009 Feb 13.
PASS: a program to align short sequences.
Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G.