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Communication Dans Un Congrès Année : 2023

HairSplitter: separating strains in metagenome assemblies with long reads

Résumé

Long read assemblers struggle to distinguish closely related strains of the same species and collapse them into a single sequence. This is very limiting when analysing a metagenome, as different strains can have important functional differences. We present the first version of a new software called HairSplitter, which recovers the strains from a strain-oblivious assembly and long reads. The originality of the method lies in a custom variant calling step that allows HairSplitter to work with erroneous reads and to separate an unknown number of haplotypes. On simulated datasets, we show that HairSplitter significantly outperforms the state of the art when dealing with metagenomes containing many strains of the same species.
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Dates et versions

hal-04272455 , version 1 (06-11-2023)

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Paternité

Identifiants

  • HAL Id : hal-04272455 , version 1

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Roland Faure, Jean-François Flot, Dominique Lavenier. HairSplitter: separating strains in metagenome assemblies with long reads. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané, France. pp.1-8. ⟨hal-04272455⟩
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