zovie1 / matchtigs

Minimum plain text representation of kmer sets

Matchtigs: minimum plain text representation of kmer sets

This is an implementation of different algorithms for computing small and minimum plain text representations of kmer sets. The algorithms expect unitigs as an input, which can e.g. be computed with BCALM2.

Features

• Compute matchtigs, greedy matchtigs or pathtigs (a heuristic similar to simplitigs)
• Compute matchtigs and greedy matchtigs with multiple threads
• Both fasta and GFA format supported

Installation via conda/mamba

Install matchtigs with

mamba install -c conda-forge -c bioconda matchtigs

Installation via cargo

Requirements

Rust >= 1.56.1, best installed via rustup.

Installation

Install matchtigs with

cargo install matchtigs

Usage

Computing matchtigs and greedy matchtigs from a fasta file and saving them as GFA (without topology):

matchtigs --fa-in unitigs.fa --matchtigs-gfa-out matchtigs.gfa --greedytigs-gfa-out greedy-matchtigs.gfa

Use the --help option to get an overview of available options.

matchtigs --help

Citation

to be added