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bioRxiv · 10.1101/2024.02.13.580067

HairSplitter: haplotype assembly from long, noisy reads

Faure, R.·Lavenier, D.·Flot, J.-F.
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Abstract

MotivationLong-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. ResultsWe 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. AvailabilityHairSplitter is freely available on GitHub at github.com/RolandFaure/HairSplitter. Contactroland.faure@irisa.fr

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Faure, R., Lavenier, D., Flot, J.-F.. 2024-02-14. HairSplitter: haplotype assembly from long, noisy reads. https://doi.org/10.1101/2024.02.13.580067

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