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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:
Restrictions to use:
Input format:
Programming languages:
Computer skills:
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
CeCILL version 2.1
Source code URL:

GASSST distribution


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GASSST support


  • Guillaume Rizk <>
  • Dominique Lavenier <>


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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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