PROJECT STATUS
Download new version of pass for Linux & Windows OS :
PASS Version 1.2
Introduction
PASS has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence.
It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments.
The program is designed to handle huge amounts of short reads generated by Solexa, SOLiD and Roche-454 technology.
The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip
false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is
performed by dynamic programming. Pass is useful for single read mapping, paired-end resequensing, small RNA discovery and RNA-seq mapping.
The details of the PASS algorithm and a comparison with other alignment programs are described in a paper by
Campagna et al.
The results indicate that PASS performs gap alignments more then 800 time faster than BLAST and several time faster than SOAP, allowing up to three gaps.
The main features of PASS are:
(1) Fast execution time
(2) Many options to modulate the sensitivity of the program
(3) Full compatibility for SOLEXA, 454 and SOLiD sequencing technologies
(4) Bases Transformations and new scoring system for color space
(5) Multi threading support
(6) Long reads alignment support
(7) Local alignment function for long reads support
(8) Client/Server TCP/IP connections support
(9) Paired-end support
(10) SNPs and IN/DELs analysis support
(11) Spliced reads alignment support
