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Global Alignment Short Sequence Search Tool GASSST

Maps reads with mismatch and indel errors at a high speed. GASSST is a short read aligner that uses the seed and extend strategy. The software’s algorithm has three stages: (i) searching for exact matching seeds between the reference genome and the query sequences; (ii) eliminating hits that have more than a user-specified number of errors, and (iii) computing the full gapped alignment with the Needleman–Wunsch (NW) algorithm. Users can specify the number of hits given per read.

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GASSST classification

GASSST specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTA
Programming languages:
C++
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
Two banks: A collection of DNA sequences of any length (from short EST sequence to full genome) and a collection of very short DNA sequences.
Operating system:
Unix/Linux, Mac OS, Windows
License:
CeCILL version 2.1
Version:
1.28
Source code URL:
http://www.irisa.fr/symbiose/projects/gassst/Gassst_v1.28.tar.gz

GASSST distribution

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No versioning.

GASSST support

Maintainers

  • Guillaume Rizk <>
  • Dominique Lavenier <>

Credits

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Publications

Institution(s)

Univ-Rennes 1/IRISA, IRISA - Symbiose Campus universitaire de Beaulieu, Rennes, France

Funding source(s)

Supported by French Agence Nationale de la Recherche BioWIC (ANR-08-SEGI-005).

Link to literature

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