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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