MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

PeerJ
Dongwan D KangZhong Wang

Abstract

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. It automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.

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Citations

Mar 10, 2016·Microbiome·Naseer SangwanJack A Gilbert
Jan 9, 2016·The ISME Journal·Matthew L BendallRex R Malmstrom
Jan 7, 2016·Frontiers in Microbiology·Brandon K B Seah, Harald R Gruber-Vodicka
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Aug 11, 2016·Current Opinion in Genetics & Development·Stephanie L SchnorrChristina Warinner
Aug 12, 2016·Translational Research : the Journal of Laboratory and Clinical Medicine·Cecilia NoeckerElhanan Borenstein
Oct 4, 2016·Nature Microbiology·Inka VanwonterghemGene W Tyson
Nov 1, 2016·Genome Announcements·Boon Fei TanJanelle R Thompson
Jun 1, 2017·Nature Communications·Christopher E LawsonDaniel R Noguera
Jan 24, 2017·Nature Communications·Peifeng JiFangqing Zhao
May 5, 2017·Nucleic Acids Research·Cedric C LacznyAndreas Keller
Dec 10, 2017·The ISME Journal·Lin-Xing ChenWen-Sheng Shu
Nov 4, 2017·Viruses·Julia VillarroelMorten Nielsen
Oct 5, 2017·Nucleic Acids Research·Yang Young LuFengzhu Sun
Apr 17, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Victoria PopicSerafim Batzoglou
Nov 24, 2017·Scientific Reports·Adrien VigneronNicolas Tsesmetzis
Nov 18, 2017·Nature Communications·Jordan C AngleKelly C Wrighton

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Datasets Mentioned

BETA
ERP000108
ERP002061

Software Mentioned

Canopy
MetaBAT
MetBAT
Megahit
GroopM
MaxBin
displaystyle
MetaHIT
Ray Meta assembler
CONCOCT

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