Section: Mathematical & Computational Biology
Topic: Biophysics and computational biology

HairSplitter: haplotype assembly from long, noisy reads

Faure, Roland1, 2  ; Lavenier, Dominique1; Flot, Jean-François2, 3 
1 Univ. Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
2 Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), Brussels, Belgium
3 Interuniversity Institute of Bioinformatics in Brussels -- (IB)2, Brussels, Belgium

Corresponding author(s): Faure, Roland (roland.faure@irisa.fr)

10.24072/pcjournal.481 - Peer Community Journal, Volume 4 (2024), article no. e96.

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Motivation: Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions. Results: We introduce a novel software, HairSplitter, designed to retrieve strains from a partially or totally collapsed assembly and long reads. The method uses a custom variant-calling process to operate with erroneous long reads and introduces a new read binning algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter recovers more strains while being faster than state-of-the-art tools, both in the cases of viruses and bacteria. Availability: HairSplitter is freely available on GitHub at https://github.com/RolandFaure/Hairsplitter (https://doi.org/10.5281/zenodo.13753481).

Published online:
DOI: 10.24072/pcjournal.481
Type: Article de recherche
Mots clés : Metagenomes, Metaviromes, Haplotyping, Genome assembly, Strain separation

Faure, Roland 1, 2; Lavenier, Dominique 1; Flot, Jean-François 2, 3

1 Univ. Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
2 Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), Brussels, Belgium
3 Interuniversity Institute of Bioinformatics in Brussels -- (IB)2, Brussels, Belgium
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Faure, Roland; Lavenier, Dominique; Flot, Jean-François. HairSplitter: haplotype assembly from long, noisy reads. Peer Community Journal, Volume 4 (2024), article  no. e96. doi : 10.24072/pcjournal.481. https://peercommunityjournal.org/articles/10.24072/pcjournal.481/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100307

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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