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Version 1.62 - 30/7/2011
(1)
input parameters in substitution of -i parameter:
-fasta ( fasta file as input)
-fastq ( fastq file as input )
-csfastq (Solid Color space fastq file)
-solved scoring system bug using SOLiD color space
-csfasta -qual (SOLiD color space csfasta and qual files)
(2)
Automatic trimming basing on bases quality analysis
(3)
SAM format supported
(4)
Automatic setting of the main parameters
(5)
Fixed bug occurred using -cpu upper to 16
(6)
Fixed BUG on SAM format for gap alignments
Download new version of pass for Linux OS :
PASS Version 1.62
Coming soon
(1) Windows and MAC binaries.
(2) RNA-seq modules in order to produce best mapping for gene prediction
(3) Modules to manage genotyping for SOLiD and ILLUMINA DNA sequenced libraries
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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 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
