bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Genome Biology
Matthew Z DeMaere, Aaron E Darling

Abstract

Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm ( https://github.com/cerebis/bin3C ).

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Citations

Dec 27, 2019·Briefings in Functional Genomics·Zhichao Xu, Jesse R Dixon
Mar 20, 2020·Genome Research·Lin-Xing ChenJillian F Banfield
Jul 17, 2020·FEMS Microbiology Reviews·Christina C SaakRachel J Dutton
Jun 4, 2020·Bioinformatics·Mikhail D MagnitovAlexander V Tyakht
Nov 13, 2019·Nature Methods·Ye Zheng, Sündüz Keleş
Feb 15, 2021·Cellular and Molecular Life Sciences : CMLS·Kevin S BlakeGautam Dantas
Feb 17, 2021·Current Opinion in Biotechnology·Neslihan TaşNicholas C Dove
Oct 18, 2019·Current Opinion in Microbiology·Travis Whitfill, Julia Oh
Oct 12, 2021·PLoS Computational Biology·Matthew Z DeMaere, Aaron E Darling
Oct 21, 2021·Molecular Ecology Resources·Bravada M HillAmanda M V Brown
Jan 13, 2022·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yuxuan DuFengzhu Sun

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Datasets Mentioned

BETA
SRR6131124

Methods Mentioned

BETA
amplicon sequencing
Hi-C
proximity ligation
pull-down

Software Mentioned

bin3C
BWA MEM
sim3C
samtools
ProxiMeta
LAST
MAG
AMI
split
Hi

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