fastp
Link to section 'Introduction' of 'fastp' Introduction
Fastp is an ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging, etc).
For more information, please check its website: https://biocontainers.pro/tools/fastp and its home page on Github.
Link to section 'Versions' of 'fastp' Versions
- 0.20.1
- 0.23.2
Link to section 'Commands' of 'fastp' Commands
- fastp
Link to section 'Module' of 'fastp' Module
You can load the modules by:
module load biocontainers
module load fastp
Link to section 'Example job' of 'fastp' 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 Fastp on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=fastp
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers fastp
fastp -i input_1.fastq -I input_2.fastq -o out.R1.fq.gz -O out.R2.fq.gz