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 and greedy matchtigs with multiple threads
• Compute Eulertigs
• Compute pathtigs (a heuristic similar to simplitigs)
• Both fasta and GFA format supported
• Output (ASCII-) bitvectors of duplicate kmers for applications that require unique kmers

Installation via conda/mamba

Install matchtigs with bash mamba install -c conda-forge -c bioconda matchtigs

Installation via cargo

Requirements

Rust >= 1.58.1, best installed via rustup.

Installation

Install matchtigs with bash cargo install matchtigs

Usage

Computing matchtigs and greedy matchtigs from a fasta file and saving them as GFA (without topology): bash matchtigs --fa-in unitigs.fa --matchtigs-gfa-out matchtigs.gfa --greedytigs-gfa-out greedy-matchtigs.gfa

Computing Eulertigs from a GFA file and saving them as both GFA (without topology) and fasta: bash matchtigs --fa-in unitigs.fa --eulertigs-gfa-out eulertigs.gfa --eulertigs-fa-out eulertigs.fa

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

Citation

preprint

Schmidt, S., Khan, S., Alanko, J., & Tomescu, A. I. (2021). Matchtigs: minimum plain text representation of kmer sets. bioRxiv. https://doi.org/10.1101/2021.12.15.472871.