Versions: [2.2.0]


Download        : docker pull ghcr.io/autamus/hisat2
Compressed Size : 32MB


HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).


Pull (Download)

To download the latest version of hisat2 run,

docker pull ghcr.io/autamus/hisat2:latest

or to download a specific version of hisat2 run,

docker pull ghcr.io/autamus/hisat2:2.2.0


To run the container as an application run,

docker run --rm ghcr.io/autamus/hisat2 hisat2 --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/hisat2 bash

Mounting volumes between the container and your machine

To access files from your machine within the hisat2 container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data ghcr.io/autamus/hisat2 hisat2 /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.


If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC hisat2 container here.