Pbmm2

Introduction

Pbmm2 is a minimap2 frontend for PacBio native data formats.

For more information, please check its website: https://biocontainers.pro/tools/pbmm2 and its home page on Github.

Versions

• 1.7.0

Commands

• pbmm2

Module

You can load the modules by:

module load biocontainers
module load pbmm2

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 Pbmm2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=pbmm2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pbmm2

pbmm2 --version

pbmm2 align hg38.fa \
    alz.polished.hq.bam alz.aligned.bam \
     -j 12 --preset ISOSEQ --sort \
     --log-level INFO