MUSET: Set of utilities for the construction of abundance unitig matrices from sequencing data - Archive ouverte HAL
Pré-Publication, Document De Travail Année : 2024

MUSET: Set of utilities for the construction of abundance unitig matrices from sequencing data

Résumé

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, which are gaining popularity for sequence-phenotype association studies, 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 reducing the number of rows in comparison 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 less than 10 hours and 20 GB memory. As a comprehensive pipeline for generating these matrices, MUSET will facilitate the extraction of biologically significant sequences, making it a valuable contribution to downstream sequencing data analyses such as genome-wide (or metagenome-wide) association studies.
Fichier principal
Vignette du fichier
muset_preprint.pdf (347.73 Ko) Télécharger le fichier
Origine Fichiers produits par l'(les) auteur(s)
Licence
Copyright (Tous droits réservés)

Dates et versions

hal-04831168 , version 1 (11-12-2024)

Licence

Copyright (Tous droits réservés)

Identifiants

  • HAL Id : hal-04831168 , version 1

Citer

Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González. MUSET: Set of utilities for the construction of abundance unitig matrices from sequencing data. 2024. ⟨hal-04831168⟩
0 Consultations
0 Téléchargements

Partager

More