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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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