adapterremoval
Link to section 'Introduction' of 'adapterremoval' Introduction
AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.
BioContainers: https://biocontainers.pro/tools/adapterremoval
Home page: https://github.com/MikkelSchubert/adapterremoval
Link to section 'Versions' of 'adapterremoval' Versions
- 2.3.3
Link to section 'Commands' of 'adapterremoval' Commands
- AdapterRemoval
Link to section 'Module' of 'adapterremoval' Module
You can load the modules by:
module load biocontainers
module load adapterremoval
Link to section 'Example job' of 'adapterremoval' 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 adapterremoval on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=adapterremoval
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers adapterremoval
AdapterRemoval --file1 input_1.fastq --file2 input_2.fastq