duplexTools

README

duplextools

duplextools is a collection of tools for processing and analyzing data generated from a range of duplex sequencing methods.

duplextools can be used to:

1. Extract and trim duplex barcodes from fastq files
2. Pair reads by molecule of origin (a read family)
3. Call variants from read families
4. Filter variant calls
5. Compute genome-wide mutation burden

Installation

1. Install go.
2. Run go install github.com/dasnellings/duplextools/...@latest

duplextools binary will be present in ~/go/bin

Supported Methods

The included tools are designed to be flexible for use with any duplex sequencing method that either

1. uses duplex barcodes inline with read1 and read2
2. the user can provide a fastq containing the duplex barcodes

duplextools has been tested (and has presets) for the following methods

• META-CS