Dockerfile for HISAT2, which "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)."
SAMtools is also installed for use in the align-RNA and align-DNA pipelines. This is because many aligners (e.g. BWA-MEM2 and HISAT2) only support outputting the uncompressed SAM, which causes a burden on the hard disk IO and limits the performace.
The HISAT2 image with SAMtools is located in UCLAHS-CDS GitHub Packages: https://github.com/orgs/uclahs-cds/packages/container/package/hisat2.
HISAT2 manual is here
| Tool | Version |
|---|---|
| HISAT2 | 2.2.1 |
| SAMTools | 1.17 |