clean_ngs [OPTIONS] -adf ADAPTER.txt -if1 IN.fq -of1 OUT.fq
clean_ngs [OPTIONS] -adf ADAPTER.txt -if1 IN_1.fq -if2 IN_2.fq -of1
OUT_1.fq -of2 OUT_2.fq

Use adapters definition file ADAPTER.txt and remove the adapters from the
input readfiles. The program writes out the cleansed reads and the
rejected reads.

-h, --help
          Displays this help message.
    --version
          Display version information
    -v, --verbose
          Verbose mode.
    -vv, --very-verbose
          Very verbose mode.

  Input / Output Parameters:
    -adf, --adapter-file FILE
          Adapter definition file. See section Adapters File Format below for
          moreinformation. Valid filetypes are: txt and dat.
    -if1, --input-file1 FILE
          Input file 1. Valid filetypes are: fastq, fq, fastq.gz, fq.gz, txt,
          txt.gz, and dat.
    -if2, --input-file2 FILE
          Input file 2. Valid filetypes are: fastq, fq, fastq.gz, fq.gz, txt,
          txt.gz, and dat.
    -of1, --output-file1 FILE
          Output file 1. Valid filetypes are: fastq, fq, fastq.gz, fq.gz, txt,
          txt.gz, and dat.
    -of2, --output-file2 FILE
          Output file 2. Valid filetypes are: fastq, fq, fastq.gz, fq.gz, txt,
          txt.gz, and dat.
    -rf1, --rejected-file1 FILE
          Rejected file 1. Valid filetypes are: fastq, fq, fastq.gz, fq.gz,
          txt, txt.gz, and dat.
    -rf2, --rejected-file2 FILE
          Rejected file 2. Valid filetypes are: fastq, fq, fastq.gz, fq.gz,
          txt, txt.gz, and dat.

  Optional Parameters:
    -l, --min-len NUM
          Minimal length of sequencing.Set to 0 to turn offminimal length
          filter. In range [0..inf]. Default: 0.
    -L, --max-len NUM
          Maximal length of sequencing.Set to 0 to turn offmaximal length
          filter. In range [0..inf]. Default: 0.
    -q3, --qual-thresh3 NUM
          Quality threshold for 3-prime trimming.Set to 0 to turn off 3-prime
          trimming. In range [0..inf]. Default: 0.
    -q5, --qual-thresh5 NUM
          Quality threshold for 5-prime trimming.Set to 0 to turn off 5-prime
          trimming. In range [0..inf]. Default: 0.

## as of the change to version 2.* this doesn't work anymore. 
# I am in the process of moving the files to the new system
# meanwhile please follow the instructions below
#This worked for me on a linux system:
#
#```Shell
## clone seqan library
#git clone https://github.com/seqan/seqan.git
## create a build directory
#mkdir seqan-trunk-build
#mkdir seqan-trunk-build/debug
#cd seqan-trunk-build/debug
## configure a DEBUG build
#cmake ../../seqan -DCMAKE_BUILD_TYPE=Debug
#cd ../../seqan
## create a sandbox environment
## The Cmake files are adjusted for that specific sandbox configuration...
#./util/bin/skel.py repository sandbox/seqan_ngs_apps
## get clean_ngs tool
##cd sandbox/seqan_ngs_apps/apps/
#git clone https://github.com/PF2-pasteur-fr/clean_ngs.git
#cd ../../../../seqan-trunk-build/debug/
## let cmake learn about the changes
#cmake .
## compile clean_ngs
#make clean_ngs
## basic test
#bin/clean_ngs -h
#```

## for version 1.4.2 (temporary soluiton)
# download old sources.
mkdir ~/seqan
cd  ~/seqan
wget http://packages.seqan.de/seqan-src/seqan-src-1.4.2.tar.gz
tar xvf seqan-src-1.4.2.tar.gz 
cd seqan-1.4.2/
# build directory structure for clean_ngs
./util/bin/skel.py repository sandbox/seqan_ngs_apps
# get clean_ngs
cd sandbox/seqan_ngs_apps/apps/
git clone https://github.com/PF2-pasteur-fr/clean_ngs.git
cd ~
mkdir -p seqan-1.4.2-build/debug
cd seqan-1.4.2-build/debug
cmake ../../seqan/seqan-1.4.2 -DCMAKE_BUILD_TYPE=Debug
make clean_ngs
bin/clean_ngs