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HSA | A heuristic splice alignment tool

Supports the alignment of both non-conservative and conservative alternative splicing (AS). HSA is an effective spliced alignment tool for RNA-Seq data. It provides two-step approach that carries out to search splice junctions: (i) the first step use BWA as an unspliced aligner to map reads and (ii) the second step is heuristic alignment stage, where a seed and extension strategy is applied for spliced alignment.

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HSA forum

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HSA classification

HSA specifications

Unique identifier:
OMICS_01944
Interface:
Command line interface
Output format:
SAM
Programming languages:
C
Stability:
Stable
Software type:
Application/Script
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes

HSA distribution

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HSA support

Documentation

Maintainer

  • Zhong Jin <>

Credits

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Publications

Institution(s)

Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing, China; Graduate University of Chinese Academy of Sciences, Beijing, China

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