ngsutils
Link to section 'Introduction' of 'ngsutils' Introduction
Ngsutils is a suite of software tools for working with next-generation sequencing datasets.
For more information, please check its website: https://biocontainers.pro/tools/ngsutils and its home page: http://ngsutils.org.
Link to section 'Versions' of 'ngsutils' Versions
- 0.5.9
Link to section 'Commands' of 'ngsutils' Commands
- ngsutils
- bamutils
- bedutils
- fastqutils
- gtfutils
Link to section 'Module' of 'ngsutils' Module
You can load the modules by:
module load biocontainers
module load ngsutils
Link to section 'Example job' of 'ngsutils' 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 Ngsutils on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ngsutils
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ngsutils
bamutils filter \
input.bam \
MQ10filtered.bam \
-mapped \
-noqcfail \
-gte MAPQ 10
bamutils stats \
-gtf genome.gtf MQ10filtered.bam \
> MQ10filtered_bamstats