fastq_trimmer

Description

fastq_trimmer is a lightweight and high-performance C++ tool for consistently hard-trimming *.fastq/*.fq (and *.fastq.gz/*.fq.gz) reads from the 5' (left) or 3' (right) ends.

Compilation

Compile the fastq_trimmer tool using the following command (as done with Ubuntu Linux):

g++ -std=c++11 fastq_trimmer.cpp -o fastq_trimmer -lz -pthread -O2

Usage

./fastq_trimmer --in/-i INPUT_DIRECTORY --out/-o OUTPUT_DIRECTORY [--N3prime/-3] 3_PRIME_TRIM_BASES [--N5prime/-5] 5_PRIME_TRIM_BASES

Options

--in or -i: Input directory containing the FastQ files to be trimmed.
--out or -o: Output directory where trimmed FastQ files will be saved.
--N3prime or -3: 3' end trim value.
--N5prime or -5: 5' end trim value.
--force or -f: Force processing even if the output file already exists.

Code Overview

The fastq_trimmer tool provides the following functionalities:

Determines if a file is likely gzipped and accordingly handles I/O.
Retrieves the list of files with supported extensions (*.fastq/*.fq/*.fastq.gz/*.fq.gz) from the input directory.
Creates the output directory if it doesn't exist.
Writes messages to a log file within the output directory.
Trims both sequence and phred qualities in all reads a fixed number of bases from the 5' and 3' ends
Dynamically handles both gzipped and non-gzipped formatted FastQs.
File processing is asynchronously parallelised.

Compilation

Before compiling, ensure you have the necessary dependencies installed:

g++ compiler (if not installed: sudo apt install build-essential)
zlib library (-lz (if not installed: sudo apt install zlib1g-dev))
POSIX threads (-pthread (if not installed: sudo apt install libpthread-stubs0-dev))

Compile the tool using the provided command after navigating to a directory containing the source file:

g++ -std=c++11 fastq_trimmer.cpp -o fastq_trimmer -lz -pthread -O2

Alternatively, you may follow this recipe as a guide:

# Download the archive
git clone https://github.com/QUB-Simpson-lab/fastq_trimmer.git
# Enter the downloaded archive
cd fastq_trimmer
# Compile
g++ -std=c++11 fastq_trimmer.cpp -o fastq_trimmer -lz -pthread -O2
# Install
sudo cp fastq_trimmer /usr/local/bin/
# Usage
fastq_trimmer --in/-i INPUT_DIRECTORY --out/-o OUTPUT_DIRECTORY [--N3prime/-3] 3_PRIME_TRIM_BASES [--N5prime/-5] 5_PRIME_TRIM_BASES

Usage Example

To trim 5 bases from the 3' end and 3 bases from the 5' end of each FastQ file within the input_dir, and save the trimmed files in the output_dir:

./fastq_trimmer --in input_dir --out output_dir --N3prime 5 --N5prime 3

License

This tool is provided under the GPLv3 License. See the LICENSE file for details.

Contact

For any questions or issues, please open an issue here on GitHub.