BarKit

[!WARNING]
This tool is under development. Please use the first release version when it becomes available.

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

Installation

cargo install barkit

Extract Command

The extract command 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 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.