clean_ngs

Yet another adapter removal program for next generation sequencing

clean_ngs - NGS Data Cleaning

SYNOPSIS

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

DESCRIPTION

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.

ADAPTER DEFINITION FILE FORMAT

The adapter sequences are defined in an adapter definition file with the extension ".txt" (dat is only allowed for Galaxy)

comment lines start with "#".

Each non-comment(non-empty) line is tab delimited

and has 7 fields (columns):

1. name of the sequence

2. sequence (N's are allowed and match any nucleotide, useful for multiplexing)

3. fraction of identity between adapter sequence and target sequence (threshold)

4. quality threshold

5. minimum length of overlap between adapter and target sequence

6. if set to >0 perform comparison with truncated adapter sequences (very time consuming)

7. if set to 1 this is a leader sequence

VERSION

clean_ngs version: 0.10 Last update Jan 2015

Installation

Basic steps:

• Follow the instructions on seqan.de to install the seqan package (https://github.com/seqan/seqan)
• Follow the instructions on creating a sandbox
• Clone clean_ngs.git to apps directory
• Update cmake configuration
• Make

## 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

Authors

The initial upload was created by Manuel Holtgrewe manuel.holtgrewe@fu-berlin.de and Bernd Jagla bernd.jagla@pasteur.fr