cutadapt
Link to section 'Introduction' of 'cutadapt' Introduction
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
For more information, please check its website: https://biocontainers.pro/tools/cutadapt and its home page: https://cutadapt.readthedocs.io/en/stable/.
Link to section 'Versions' of 'cutadapt' Versions
- 3.4
- 3.7
Link to section 'Commands' of 'cutadapt' Commands
- cutadapt
Link to section 'Module' of 'cutadapt' Module
You can load the modules by:
module load biocontainers
module load cutadapt
Link to section 'Example job' of 'cutadapt' 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 Cutadapt on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cutadapt
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cutadapt
cutadapt -a AACCGGTT -o output.fastq input.fastq