MetaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics.

ABSTRACT: The availability of large metagenomic data offers great opportunities for the population genomic analysis of uncultured organisms, which represent a large part of the unexplored biosphere and play a key ecological role. However, the majority of these organisms lack a reference genome or transcriptome, which constitutes a technical obstacle for classical population genomic analyses. We introduce the metavariant species (MVS) model, in which a species is represented only by intra-species nucleotide polymorphism. We designed a method combining reference-free variant calling, multiple density-based clustering and maximum-weighted independent set algorithms to cluster intra-species variants into MVSs directly from multisample metagenomic raw reads without a reference genome or read assembly. Th

SUBMITTER: Laso-Jadart R 

PROVIDER: S-EPMC7773188 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature