GASSST - Global Alignment Short Sequence Search Tool

GASSST : Global Alignment Short Sequence Search Tool

GASSST is a free software distributed under the terms of the

Overview

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.

Download

This software was developed using version 4.1.2 of the GNU gcc compiler on a Linux Fedora 8 distribution.

Support for MacOS X and Windows is in progress ....

Authors

GASSST is developed whithin the bioinformatics Symbiose group at IRISA-INRIA, Rennes, France.

Current and former development contributors