HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

For more information, please check its website: https://biocontainers.pro/tools/hisat2 and its home page on Github.


  • 2.2.1


  • extract_exons.py

  • extract_splice_sites.py

  • hisat2

  • hisat2-align-l

  • hisat2-align-s

  • hisat2-build

  • hisat2-build-l

  • hisat2-build-s

  • hisat2-inspect

  • hisat2-inspect-l

  • hisat2-inspect-s

  • hisat2_extract_exons.py

  • hisat2_extract_snps_haplotypes_UCSC.py

  • hisat2_extract_snps_haplotypes_VCF.py

  • hisat2_extract_splice_sites.py

  • hisat2_read_statistics.py

  • hisat2_simulate_reads.py


You can load the modules by:

module load biocontainers
module load hisat2

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run HISAT2 on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 1
#SBATCH --job-name=hisat2
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers hisat2

hisat2-build genome.fa genome

# for single-end FASTA reads DNA alignment
hisat2 -f -x genome -U reads.fa -S output.sam --no-spliced-alignment

# for paired-end FASTQ reads alignment
hisat2 -x genome -1 reads_1.fq -2 read2_2.fq -S output.sam