==== description ====
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]], software usage examples [[https://adapterremoval.readthedocs.io/en/latest/examples.html]] .

==== software version ====
Bellow description covers AdapterRemoval version 2.3.1 .

==== prepare software ====
Login to anthill23, start interactive session in which download and compile AdapterRemoval ((this will take 5 minutes)):

  @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, compitation will end with message
  #  Linking executable build/AdapterRemoval
  #exit interactive mode when finished with exit command
  exit


==== sbatch example ====
This description assumes that above step ( prepare software ) were done beforehand. \\
Bellow slurm job creates temporary folder in your home folder (like ''tmp.AtrQrrJi3W''), then downloads file ''090413_I352_FC31307AAXX_L6_SORssqRADDHAAPE_1.fq.gz'' and run it with AdapterRemoval software. This job will take about 10 minutes, inspect job output ex.: ''slurm-1949.out'' for AdapterRemoval output messages.

File ''adapterremoval_test.batch'' :

<code>
#!/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


</code>

==== performance tests ====
None. At this time.