MUSET: set of utilities for constructing abundance unitig matrices from sequencing data

Abstract

MUSET is a novel set of utilities designed to efficiently construct abundance unitig matrices from sequencing data. Unitig matrices extend the concept of k-mer matrices by merging overlapping k-mers that unambiguously belong to the same sequence. MUSET addresses the limitations of current software by integrating k-mer counting and unitig extraction to generate unitig matrices containing abundance values, as opposed to only presence–absence in previous tools. These matrices preserve variations between samples while reducing disk space and the number of rows compared to k-mer matrices. We evaluated MUSET’s performance using datasets derived from a 618-GB collection of ancient oral sequencing samples, producing a filtered unitig matrix that records abundances in <10h and 20 GB memory. Availability and implementation: MUSET is open source and publicly available under the AGPL-3.0 licence in GitHub at https://github.com/CamilaDuitama/muset. Source code is implemented in Cþþ and provided with kmat_tools, a collection of tools for processing k-mer matrices. Version v0.5.1 is available on Zenodo with DOI 10.5281/zenodo.14164801.