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Sequence Search and Alignment by Hashing Algorithm SSAHA

A pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

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SSAHA forum

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SSAHA classification

SSAHA specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Version:
2.0
Maintained:
Yes
Interface:
Command line interface
Biological technology:
Illumina, Roche
Computer skills:
Advanced
Stability:
Stable

SSAHA distribution

versioning

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No versioning.

SSAHA support

Maintainer

  • Zemin Ning <>

Credits

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Publications

Institution(s)

Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Link to literature

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