Yet another adapter removal program for next generation sequencing
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.
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):
-
name of the sequence
-
sequence (N's are allowed and match any nucleotide, useful for multiplexing)
-
fraction of identity between adapter sequence and target sequence (threshold)
-
quality threshold
-
minimum length of overlap between adapter and target sequence
-
if set to >0 perform comparison with truncated adapter sequences (very time consuming)
-
if set to 1 this is a leader sequence
clean_ngs version: 0.10 Last update Jan 2015
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
The initial upload was created by Manuel Holtgrewe [email protected] and Bernd Jagla [email protected]