MUSET: set of utilities for constructing abundance unitig matrices from sequencing data [sequence analysis]
Résumé
Summary: 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 <10 h 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 C++ 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.
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Cite 10.5281/zenodo.14164801 Ouvrage Vicedomini, R., Andreace, F., Dufresne, Y., Chikhi, R., & Duitama González, C. (2024). MUSET (Version 0.5.1). Zenodo. https://doi.org/10.5281/ZENODO.14164801
MUSET is open source and implemented in C++. It is provided with kmat_tools, a collection of tools for processing -mer matrices. MUSET v0.5.1 is publicly available on Zenodo with DOI 10.5281/zenodo.14164801. The latest available version with the instructions for installing and running it are available at https://github.com/CamilaDuitama/muset.