Version 2.30 - 05/2016
New - New improved algorithm for SOLID BIS-seq mapping
Minor bug fixed
Download the new version of pass for Linux OS :
Download the user manual :
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 ILLUMINA, 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.
Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G.
PASS: a program to align short sequences.
Bioinformatics. 2009 Apr 1;25(7):967-8. doi: 10.1093/bioinformatics/btp087. Epub 2009 Feb 13
Campagna D, Telatin A, Forcato C, Vitulo N, Valle G.
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Bioinformatics. 2013 Jan 15;29(2):268-70. doi:
10.1093/bioinformatics/bts675. Epub 2012 Nov 17.