Htslib

Introduction

Htslib is a C library for high-throughput sequencing data formats.

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

Versions

1.14
1.15
1.16
1.17

Commands

bgzip
htsfile
tabix

Module

You can load the modules by:

module load biocontainers
module load htslib

Example job

Warning

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 Htslib on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=htslib
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers htslib

tabix sorted.gff.gz chr1:10,000,000-20,000,000