PASS: a program to align short sequences

Abstract

Standard DNA alignment programs are inadequate to manage the data produced by new generation DNA sequencers. To answer this problem, we developed PASS with the objective of improving execution time and sensitivity when compared with other available programs. 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 and 12 bases) as well as an index of the precomputed scores of short words (typically seven and eight bases) aligned against each other. After building the genomic index, the program scans every query sequence performing three steps: (1) it finds matching seed words in the genome; (2) for every match checks the precomputed alignment of the short flanking regions; (3) if passes step 2, then it performs an exact dynamic alignment of a narrow region around the match. The performance of the program is very striking both for sensitivity and speed. For instance, gap alignment is achieved hundreds of times faster than BLAST and several times faster than SOAP, especially when gaps are allowed. Furthermore, PASS has a higher sensitivity when compared with the other available programs. Source code and binaries are freely available for download at http://pass.cribi.unipd.it, implemented in C++and supported on Linux and Windows.