CRwiki

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. Software page : https://github.com/MikkelSchubert/adapterremoval .

Bellow description covers AdapterRemoval version 2.3.1 .

https://adapterremoval.readthedocs.io/en/latest/examples.html

Login to anthill23, start interactive session in which download and compile AdapterRemoval ¹⁾:

@anthill23:~$ srun -n 2 --mem=4G --pty bash -l

mkdir ~/anthill23_soft/
cd ~/anthill23_soft/
wget -O adapterremoval-2.3.1.tar.gz https://github.com/MikkelSchubert/adapterremoval/archive/v2.3.1.tar.gz
tar xvzf adapterremoval-2.3.1.tar.gz
cd adapterremoval-2.3.1

make -j${SLURM_NPROCS}

#read output and exit interactive mode when finished
exit

This description assumes that above step ( prepare software ) were done beforehand.

File adapterremoval_test.batch .

#!/bin/bash -l
#SBATCH --partition=test
#SBATCH --ntasks=2
#SBATCH --mem 4G
#SBATCH --job-name AdapterRemoval_test

#prepare temporary folder
cd `mktemp -d -p ~/`

#download fq file
wget wget ftp://download.big.ac.cn/SorghumVB/fastq/090413_I352_FC31307AAXX_L6_SORssqRADDHAAPE_1.fq.gz

#export path to AdapterRemoval binary
export PATH=$PATH:/home/users/${USER}/anthill23_soft/adapterremoval-2.3.1/build

#use AdapterRemoval software
AdapterRemoval --file1 090413_I352_FC31307AAXX_L6_SORssqRADDHAAPE_1.fq.gz --qualitybase 64

None. At this time.