GASSST : Global Alignment Short Sequence Search Tool
GASSST is a free software distributed under the terms of the
CECILL version 2 License
GASSST article is now available!
GASSST finds global alignments of short DNA sequences against large DNA banks.
GASSST strong point is its ability to perform fast gapped alignments.
It works well for both short and longer reads. It currently has been tested for reads up to 500bp.
The software is freely available for download under the CECILL version 2 License.
Usage example :
For alignments with 90 % similarity minimum
Gassst -d bank.fasta -i query.fasta -o results -p 90
Then call "gassst_to_sam" if you want to convert output to SAM format :
./gassst_to_sam results results.sam
The program takes as inputs 2 banks in FASTA format :
bank_file : a collection of DNA sequences of any length (from short EST sequence to full genome).
query file : a collection of very short DNA sequences.
For the complete list of options, see the readme file.
Source Gassst v 1.28 : [tar.gz]
This software was developed using version 4.1.2 of the GNU gcc compiler on a Linux Fedora 8 distribution.
New in version 1.28 (01/08/11):
A few bugs were fixed (particularly in gassst_to_sam.cpp).
New in version 1.27 (03/09/11):
Fixed bug and memory leaks for very large reads.
New in version 1.266 (03/04/11):
gassst to sam now output results in the same ordre as the query file
option -g now specifies maximum number of gaps by percentage of the query length.
New in version 1.265 (02/16/11):
Added option in gassst_to_sam to output multiple results per read in the sam format, not only the best one.
Support for even larger reads.
Bugs corrected in version 1.262 (10/21/10):
bug in sam format generation causing read sequences to be sometimes erroneously reversed when it should not and vice-versa.
fixed crashes for extra long ( > 1000 nt ) reads.
New in version 1.24 :
added support for processors without ssse3 (-amd flag at compilation)
New in version 1.23 :
added tool to convert to sam format.
Automatic seed length calculation.
GASSST is developed whithin the bioinformatics Symbiose group at IRISA-INRIA, Rennes, France.
Current and former development contributors