Matcha

Matcha is a python library to do fast barcode matching of short DNA sequences. It supports multi-threaded fastq input and output, and allows for arbitrary user-specified barcodes and filtering criteria.

Installation

Requirements: Python >=3.5, pybind11, numpy, pandas

Installation can be done through pip using the github source:

pip install git+https://github.com/GreenleafLab/matcha.git

Documentation

Example usage and reference documentation are available here:

• Quick Example

• Reference Documentation

What Matcha doesn’t do

Matcha aims to provide simple, fast, and flexible DNA barcode matching in python. However, it currently cannot handle:

• Probabilistic error correction (e.g. using quality scores or priors about barcode abundance)

• Variable-length barcodes

• Barcodes where the read position is not known in advance

• UMI correction where the set of valid sequences is not known in advance (potentially coming soon)