HISAT2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a reference genome. It is widely used for spliced alignment of RNA-seq reads.

• HISAT2
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source under GNU GPLv3.

Available

• Roihu: 2.2.1, via the bio-apps module.

Usage

HISAT2 is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the HISAT2 module:

module load bio-apps/v202603
module load hisat2/2.2.1

First build an index of the reference genome:

hisat2-build genome.fa genome_index

Then align reads (here paired-end):

hisat2 -p 8 -x genome_index -1 read1.fq -2 read2.fq -S output.sam

Example batch script

#!/bin/bash
#SBATCH --job-name=hisat2
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load hisat2/2.2.1

hisat2 -p $SLURM_CPUS_PER_TASK -x genome_index -1 read1.fq -2 read2.fq -S output.sam

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• HISAT2 home page

Do you find this page useful?

Yes

Thank you for your feedback!

No

Thank you! Your feedback is appreciated.

Please let us know how we could improve this page by contacting us or by creating an issue in GitHub. You can also edit this page yourself and contribute your improvements by creating a pull request.