MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39898792.
- Also identified by DOI 10.1093/bioinformatics/btaf054 and PMC identifier 11897428.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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 <10 h and 20 GB memory. 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.
Medical subject headings
- Software
- Sequence Analysis, DNA
- High-Throughput Nucleotide Sequencing
- Computational Biology