Article Dans Une Revue Bioinformatics Année : 2025

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.

Fichier principal
Vignette du fichier
btaf054.pdf (1.17 Mo) Télécharger le fichier
Origine Publication financée par une institution
Licence
DOI

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.

Dates et versions

hal-04831168 , version 1 (11-12-2024)
hal-04831168 , version 2 (28-03-2025)

Licence

Identifiants

Citer

Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González. MUSET: set of utilities for constructing abundance unitig matrices from sequencing data [sequence analysis]. Bioinformatics, 2025, 41 (3), pp.1-5. ⟨10.1093/bioinformatics/btaf054⟩. ⟨hal-04831168v2⟩
661 Consultations
388 Téléchargements

Altmetric

Partager

  • More