FICHA · AUR

hisat2

A fast and sensitive alignment program for mapping next-generation sequencing reads against genomes

  • scientific-tool
  • CLI
  • TERMINAL
  • BIOINFORMATICS
  • Launchable
  • Runs in terminal
official+codex · reviewed · Jun 1, 2026 description in en

Description

Next-generation sequencing reads can be aligned against genomes for RNA-seq and other genomics analysis workflows.

It is useful for bioinformaticians who need fast, sensitive mapping before quantification, variant exploration, or downstream statistics. Scientific accuracy depends on reference indexes, read quality, parameters, and proper interpretation of alignment outputs.

How to run

hisat2

Commands: hisat2

Permissions

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