HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs.

ABSTRACT:

Motivation

Metagenomic binning aims to retrieve microbial genomes directly from ecosystems by clustering metagenomic contigs assembled from short reads into draft genomic bins. Traditional shotgun-based binning methods depend on the contigs' composition and abundance profiles and are impaired by the paucity of enough samples to construct reliable co-abundance profiles. When applied to a single sample, shotgun-based binning methods struggle to distinguish closely related species only using composition information. As an alternative binning approach, Hi-C-based binning employs metagenomic Hi-C technique to measure the proximity contacts between metagenomic fragments. However, spurious inter-species Hi-C contacts inevitably generated by incorrect ligations of DNA fragments between spe

SUBMITTER: Du Y 

PROVIDER: S-EPMC9154269 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature