/PE-Trimmer

An efficient trimming algorithm based on multi-feature fusion scoring model for NGS data

Primary LanguageJava

Latest Version

Please see the latest version of PE-Trimmer:https://github.com/bioinfomaticsCSU/PE-Trimmer

License

Copyright (C) 2017 Jianxin Wang(jxwang@mail.csu.edu.cn), Xingyu Liao(liaoxingyu@csu.edu.cn)

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, see http://www.gnu.org/licenses/.

Jianxin Wang(jxwang@mail.csu.edu.cn), Xingyu Liao(liaoxingyu@csu.edu.cn) School of Information Science and Engineering Central South University ChangSha CHINA, 410083

Installation and operation of PE-Trimmer

Dependencies

When running PE-Trimmer from GitHub source the following tools are required:

Add system environment variables

The user can modify the system environment variables with the following commands:

vim /etc/profile

export JAVA_HOME="/usr/local/jdk1.8.0_20/bin"

export DSK_HOME="/home/.../dsk-2.1.0-Linux/bin"

export PATH="$JAVA_HOME:$DSK_HOME:$PATH"

source /etc/profile

Install PE-Trimmer

PE-Trimmer automatically compiles all its sub-parts when needed (on the first use). Thus, installation is not required.

Run PE-Trimmer.

  1. Load library files into PE-Trimmer

    Before running PE-Trimmer, we need to load the library files into lib folder(/home/.../PE-Trimmer/lib/).

    For example:

    One library (The library is composed of paired-end reads).

    /home/.../PE-Trimmer/lib/frag_1.fastq (The left mate reads of the library)

    /home/.../PE-Trimmer/lib/frag_2.fastq (The right mate reads of the library)

  2. Edit the configuration

    Before running PE-Trimmer, we also need to configure the file of config.txt(/home/.../PE-Trimmer/config.txt).

    For example:

    home=/homed/liaoxingyu/PE-Trimmer

    lib_left_name=reads_1

    lib_right_name=reads_2

    Readlength=100

    WindowSize=11

    UserThreshold=0.3

    • 'home': The working directory of PE-Trimmer.
    • 'lib_left_name': The name of the left fastq file.
    • 'lib_right_name': The name of the right fastq file.
    • 'Readlength': The average length of reads.
    • 'WindowSize': Window size setting during trimming.
    • 'UserThreshold': Trimming threshold. The default value of it is 0.3. It can also be manually set by the user.

  3. Run the following command to start PE-Trimmer.

    cd /home/.../PE-Trimmer

    ./run.sh

    If the system prompts "operation not permitted" , we need to run the following commands to modify the permissions of PE-Trimmer folder at this time.

    cd ..

    chmod -R 777 PE-Trimmer

    cd PE-Trimmer

Output.

/home/.../PE-Trimmer/TrimInformations/Trimed.paired_right.fq

/home/.../PE-Trimmer/TrimInformations/Trimed.paired_left.fq

/home/.../PE-Trimmer/TrimInformations/Unpaired_left.fq

/home/.../PE-Trimmer/TrimInformations/Unpaired_right.fq

Evaluate the trimming effect of PE-Trimmer.

cd /home/.../PE-Trimmer/Test

./Test.sh

The users need to read the instruction in the "Test" foler.