DNAbc

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

Installation

GitHub

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

DockerHub

docker pull ctbushman/dnabc:latest
docker run --rm --name dnabc dnabc dnabc -h

Usage

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

dnabc 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.