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GSNAP

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily long length. GSNAP can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. GSNAP also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state.

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GSNAP forum

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GSNAP classification

GSNAP specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
SAM
Programming languages:
C, Perl
Stability:
Stable
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes

GSNAP distribution

versioning

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No versioning.

GSNAP support

Maintainer

  • Thomas Wu <>

Credits

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Publications

Institution(s)

Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA

Link to literature

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