skewer
Link to section 'Introduction' of 'skewer' Introduction
Skewer is a fast and accurate adapter trimmer for paired-end reads.
For more information, please check its website: https://biocontainers.pro/tools/skewer and its home page on Github.
Link to section 'Versions' of 'skewer' Versions
- 0.2.2
Link to section 'Commands' of 'skewer' Commands
- skewer
Link to section 'Module' of 'skewer' Module
You can load the modules by:
module load biocontainers
module load skewer
Link to section 'Example job' of 'skewer' 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 Skewer on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=skewer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers skewer
skewer -l 50 -m pe -o skewerQ30 --mean-quality 30 \
--end-quality 30 -t 10 -x TruSeq3-PE.fa \
input_1.fastq input_2.fastq