HISAT2

A tool to map DNA and RNA sequences to one or more genomes. The HISAT2 algorithm uses an extension of the Burrows-Wheeler transform (BWT) to generate graphs, a new graph FM index (GFM), and a Hierarchical Graph FM index (HGFM) to index a whole-genome and population of genomes.

Topic

RNA-seq; Sequencing;Mapping

Detail

  • Operation: Sequence alignment;Mapping

  • Software interface: Command-line user interface

  • Language: Python

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 2.1.0

  • Credit: he National Human Genome Research Institute (US National Institutes of Health)

  • Input: -

  • Output: -

  • Contact: Ben Langmead langmea@cs.jhu.edu | Daehwan Kim infphilo@gmail.com | Steven L Salzberg salzberg@jhu.edu

  • Collection: -

  • Maturity: Mature

Publications

  • HISAT: a fast spliced aligner with low memory requirements.
  • Kim D, et al. HISAT: a fast spliced aligner with low memory requirements. HISAT: a fast spliced aligner with low memory requirements. 2015; 12:357-60. doi: 10.1038/nmeth.3317
  • https://doi.org/10.1038/nmeth.3317
  • PMID: 25751142
  • PMC: PMC4655817

Download and documentation

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