Identify DNA barcodes in FASTQ data files and write demultiplexed data.

Install by cloning this repository and using pip.

git clone https://github.com/PennChopMicrobiomeProgram/dnabc.git
cd dnabc
pip install .

The Python library provides a command-line program, dnabc.py. The program takes three positional arguments: a file of barcodes, a FASTQ file of forward reads, and a FASTQ file of reverse reads.

dnabc.py barcodes.txt myreads_R1.fastq myreads_R2.fastq

The FASTQ files can be compressed with gzip, and are treated as compressed files if the filename ends with .gz.

The file of barcode sequences should be in tab-separated format, where the first column gives the sample name and the second column gives the barcode DNA sequence. The barcode file should have column names in the first line. After the header, lines starting with # and blank lines are ignored. The barcode file can contain additional columns, as long as the sample name and barcode sequence are in the first two columns.