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rgsplitter

rgsplitter - Illumina FastQ Read Group Splitter

README.md for rgsplitter tool

Overview

This repository contains a Docker component rgsplitter, a Python script designed to split Illumina FastQ files by read groups. It's optimized for handling large datasets and provides a user-friendly command-line interface for bioinformatics data processing.

Features

  • Read Group Splitting: Automatically identifies and segregates read groups within FastQ files, a crucial feature for multiplexed sequencing data.
  • Efficient Data Handling: Optimized for large FastQ files, ensuring quick processing times and low memory usage.
  • User-Friendly Interface: Simple command-line interface with clear argument requirements.
  • Quality Control: Implements checks for data consistency after processing.

Requirements

  • Docker environment.

Installation and Setup

  1. Clone the Repository: 
    git clone git@github.com:Genebio/rgsplitter.git
  2. Build the Docker Image: Assuming the Dockerfile is in the same directory: 
    docker build -t rgsplitter:1.0.0 .

Usage

To run the script within a Docker container, use the following command:

docker run --rm -it \
    -v [local-directory-path]:/mnt \
    rgsplitter:1.0.0 \
    --fastq1 /mnt/[fastq-file-1] \
    --fastq2 /mnt/[fastq-file-2] \
    --output-basename /mnt/[output-basename] \
    --readgroups-txt /mnt/[readgroups-txt-file]

Replace [local-directory-path], [fastq-file-1], [fastq-file-2], [output-basename], and [readgroups-txt-file] with your specific file paths and names.

Command-line Arguments

  • --fastq1: Path to the input fastq.gz file (SE or PE pair 1).
  • --fastq2: Path to the input fastq.gz file (PE pair 2), if applicable.
  • --output-basename: The output prefix for processed files.
  • --readgroups-txt: Path to the output file listing unique readgroups.
  • --ignore-warnings: Option to ignore warnings in case of inconsistent results.

Troubleshooting and Support

For issues and questions regarding the use of this tool, please refer to the issue tracker in the GitHub repository or contact genebio91@gmail.com.

Contribution

Contributions to this project are welcome. Please fork the repository and submit a pull request with your changes.

Usage example on small test fastq files

docker run --rm -it \
    -v $(pwd)/test/:/mnt \
    rgsplitter:1.0.0 \
    --fastq1 /mnt/RNASeq-tumor_1k_1.fastq.gz \
    --fastq2 /mnt/RNASeq-tumor_1k_2.fastq.gz \
    --output-basename /mnt/RNASeq-tumor \
    --readgroups-txt /mnt/RNASeq-tumor-readgroups.txt

Log Output

  • /usr/local/src/run.py | line 189 | INFO | TEMPDIR = '/tmp', OUTPREFIX = '/root'
  • /usr/local/src/run.py | line 192 | INFO | Starting program with the following arguments: {'fastq1': '/mnt/RNASeq-tumor_1k_1.fastq.gz', 'fastq2': '/mnt/RNASeq-tumor_1k_2.fastq.gz', 'output_basename': '/mnt/RNASeq-tumor', 'readgroups_txt': '/mnt/RNASeq-tumor-readgroups.txt', 'ignore_warnings': False}
  • /usr/local/src/run.py | line 165 | INFO | '/mnt/RNASeq-tumor-readgroups.txt' file content: ['A01231:742:HHMCWDRX3:1', 'A01231:742:HHMCWDRX3:2']
  • /usr/local/src/run.py | line 124 | INFO | Splitting /mnt/RNASeq-tumor_1k_1.fastq.gz by 'A01231:742:HHMCWDRX3:1'...
  • /usr/local/src/run.py | line 56 | INFO | Running the following subprocess command: 'seqkit grep -rp ^A01231:742:HHMCWDRX3:1 -j 8 -o /mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:1_1.fastq.gz /mnt/RNASeq-tumor_1k_1.fastq.gz'
  • /usr/local/src/run.py | line 127 | INFO | Successfully splitted '/mnt/RNASeq-tumor_1k_1.fastq.gz' by 'A01231:742:HHMCWDRX3:1' to '/mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:1_1.fastq.gz'
  • /usr/local/src/run.py | line 124 | INFO | Splitting /mnt/RNASeq-tumor_1k_2.fastq.gz by 'A01231:742:HHMCWDRX3:1'...
  • /usr/local/src/run.py | line 56 | INFO | Running the following subprocess command: 'seqkit grep -rp ^A01231:742:HHMCWDRX3:1 -j 8 -o /mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:1_2.fastq.gz /mnt/RNASeq-tumor_1k_2.fastq.gz'
  • /usr/local/src/run.py | line 127 | INFO | Successfully splitted '/mnt/RNASeq-tumor_1k_2.fastq.gz' by 'A01231:742:HHMCWDRX3:1' to '/mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:1_2.fastq.gz'
  • /usr/local/src/run.py | line 124 | INFO | Splitting /mnt/RNASeq-tumor_1k_1.fastq.gz by 'A01231:742:HHMCWDRX3:2'...
  • /usr/local/src/run.py | line 56 | INFO | Running the following subprocess command: 'seqkit grep -rp ^A01231:742:HHMCWDRX3:2 -j 8 -o /mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:2_1.fastq.gz /mnt/RNASeq-tumor_1k_1.fastq.gz'
  • /usr/local/src/run.py | line 127 | INFO | Successfully splitted '/mnt/RNASeq-tumor_1k_1.fastq.gz' by 'A01231:742:HHMCWDRX3:2' to '/mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:2_1.fastq.gz'
  • /usr/local/src/run.py | line 124 | INFO | Splitting /mnt/RNASeq-tumor_1k_2.fastq.gz by 'A01231:742:HHMCWDRX3:2'...
  • /usr/local/src/run.py | line 56 | INFO | Running the following subprocess command: 'seqkit grep -rp ^A01231:742:HHMCWDRX3:2 -j 8 -o /mnt/RNASeq-tumor-A01231:742:HHMCWDRX3:2_2.fastq.gz /mnt/RNASeq-tumor_1k_2.fastq
  • /usr/local/src/run.py | line 81 | INFO | Checking if '/mnt/RNASeq-tumor_1k_1.fastq.gz' is consistent...
  • /usr/local/src/run.py | line 93 | INFO | Consistency check passed for '/mnt/RNASeq-tumor_1k_1.fastq.gz'
  • /usr/local/src/run.py | line 81 | INFO | Checking if '/mnt/RNASeq-tumor_1k_2.fastq.gz' is consistent...
  • /usr/local/src/run.py | line 93 | INFO | Consistency check passed for '/mnt/RNASeq-tumor_1k_2.fastq.gz'
  • /usr/local/src/run.py | line 175 | INFO | Consistency check passed for all input fastq files.
  • /usr/local/src/run.py | line 196 | INFO | Run completed successfully.