Paired end FASTQ demultiplexing

Demultiplex paired end reads by fixed position barcodes. This library requires Boost C++ libraries and a compiler supporting C++17. This software is work in progress.

Installation

This software has successfully compiled on:

• GCC 6.3.0
• clang 6.0.0

To compile the program:

git clone https://github.com/Shians/fastq-demultiplex.git
cd fastq-demultiplex
make

The binaries will be in the bin folder. Manually place this in the path or run

make install

to install to /usr/local/bin, otherwise run

make install prefix=/some/path  # installs to /some/path/bin

Usage

Basic usage:

paired_fastq_demultiplex \
    --bc "sample_index.csv" \    # comma separated filename, barcode pairs. i.e. "sample1,AGATGATG"
    --r1 "sample_R1.fastq.gz" \  # R1 fastq file
    --r2 "sample_R2.fastq.gz" \  # R2 fastq file
    --first 7 \                  # Barcode starting position (1-indexed). Position on R1 unless --r2bc argument is set
    --last 14 \                  # Barcode ending position
    -o split_files               # Folder to store output

See paired_fastq_demultiplex --help for details.

Files will be created for each entry in sample_index.csv, all reads with no barcode match will be placed in Undetermined_R1.fastq.gz and Undetermined_R2.fastq.gz.

Warnings

• On MacOS the number of files that can be opened by terminal is limited to 256, this program will fail silently and output fewer than expected files.
  • Easiest way to fix this is by installing iTerm2 and running this program inside. NOTE iTerm versions after 3.2.9 have set the file limit to match the macOS default of 256. For more than 128 barcodes, you will need to use an older version from here.
  • Check your files open limit using ulimit -n.
• This is still a work in progress, please report any bugs you find using the issues tab.