pbmm2
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'pbmm2' Versions
- 1.7.0
Link to section 'Commands' of 'pbmm2' Commands
- pbmm2
Link to section 'Module' of 'pbmm2' Module
You can load the modules by:
module load biocontainers
module load pbmm2
Link to section 'Example job' of 'pbmm2' 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 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