BarKit

BarKit (Barcodes ToolKit) is a toolkit designed for manipulating FASTQ barcodes.

Installation

From crates.io

Barkit can be installed from crates.io using cargo. This can be done with the following command:

cargo install barkit

Build from source

1. Clone the repository:

git clone https://github.com/nsyzrantsev/barkit
cd barkit/

2. Build:

cargo build --release && sudo mv target/release/barkit /usr/local/bin/

Extract subcommand

The extract subcommand is designed to parse barcode sequences from FASTQ reads using approximate regex matching based on a provided pattern.

All parsed barcode sequences are moved to the read header with base quality, separated by colons:

@SEQ_ID UMI:ATGC:???? CB:ATGC:???? SB:ATGC:????

• UMI: Unique Molecular Identifier (Molecular Barcode)
• CB: Cell Barcode
• SB: Sample Barcode

Examples

Parse the first twelve nucleotides as a UMI from each forward read:

barkit extract -1 <IN_FASTQ1> -2 <IN_FASTQ2> -p "^(?P<UMI>[ATGCN]{12})" -o <OUT_FASTQ1> -O <OUT_FASTQ2>

Parse the first sixteen nucleotides as a cell barcode from each reverse read before the atgccat adapter sequence:

barkit extract -1 <IN_FASTQ1> -2 <IN_FASTQ2> -P "^(?P<CB>[ATGCN]{16})atgccat" -o <OUT_FASTQ1> -O <OUT_FASTQ2>

[!NOTE] Use lowercase letters for fuzzy match patterns.