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Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers

Guillaume Scholz 1 Benjamin Linard 1, 2 Nikolai Romashchenko 1 Eric Rivals 1 Fabio Pardi 1
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Motivation: Novel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically distinct viral types. Here, we consider the task of screening large collections of sequences for such novel recombinants. A number of methods already exist for this task. However, these methods rely on complex models and heavy computations that are not always practical for a quick scan of a large number of sequences. Results: We have developed SHERPAS, a new program to detect novel recombinants and provide a first estimate of their parental composition. Our approach is based on the precomputation of a large database of ‘phylogenetically-informed k-mers’, an idea recently introduced in the context of phylogenetic placement in metagenomics. Our experiments show that SHERPAS is hundreds to thousands of times faster than existing software, and enables the analysis of thousands of whole genomes, or long-sequencing reads, within minutes or seconds, and with limited loss of accuracy. Availability and implementation: The source code is freely available for download at https://github.com/phylo42/sherpas. Supplementary information: Supplementary data are available at Bioinformatics online.
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https://hal.archives-ouvertes.fr/hal-03094833
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Submitted on : Tuesday, January 12, 2021 - 1:15:29 PM
Last modification on : Wednesday, November 3, 2021 - 7:44:40 AM
Long-term archiving on: : Tuesday, April 13, 2021 - 6:32:42 PM

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Guillaume Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio Pardi. Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers. Bioinformatics, Oxford University Press (OUP), 2020, pp.#btaa1020. ⟨10.1093/bioinformatics/btaa1020⟩. ⟨hal-03094833⟩

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