sambamba
Link to section 'Introduction' of 'sambamba' Introduction
Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.
For more information, please check its website: https://biocontainers.pro/tools/sambamba and its home page on Github.
Link to section 'Versions' of 'sambamba' Versions
- 0.8.2
Link to section 'Commands' of 'sambamba' Commands
- sambamba
Link to section 'Module' of 'sambamba' Module
You can load the modules by:
module load biocontainers
module load sambamba
Link to section 'Example job' of 'sambamba' 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 Sambamba on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sambamba
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers sambamba
sambamba view --reference-info input.bam
sambamba view -c -F "mapping_quality >= 40" input.bam