MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

PeerJ
Dongwan D KangZhong Wang

Abstract

We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available ...Continue Reading

References

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Citations

Jan 23, 2020·Nature·Frederik SchulzTanja Woyke
Apr 7, 2020·Nature Communications·Mohammad MoniruzzamanFrank O Aylward
Jan 11, 2020·Microbiology Resource Announcements·Meghan DonovanKathryn M Jones
Mar 14, 2020·Bioinformatics·Vijini MallawaarachchiYu Lin
Jun 20, 2020·FEMS Microbiology Reviews·Francesca De FilippisDanilo Ercolini
Jul 14, 2020·Bioinformatics·Anuradha WickramarachchiYu Lin
May 7, 2020·The ISME Journal·Hans K CarlsonAdam M Deutschbauer
Jul 1, 2020·Annual Review of Microbiology·Felicia N New, Ilana L Brito
May 27, 2020·Nature Communications·Edoardo PasolliDanilo Ercolini
Sep 18, 2020·The ISME Journal·Andrew M LongJed A Fuhrman
May 7, 2020·Environmental Microbiology·Maeva FinckerAlfred M Spormann
Jul 25, 2020·Microbial Genomics·Ana Elena Pérez-CobasCarmen Buchrieser
Aug 10, 2020·Nature Communications·Shanshan YangYu Zhang
Feb 18, 2020·Microbiome·Anissa GriebBernhard M Fuchs
Jun 18, 2020·MSystems·Frank O Aylward, Alyson E Santoro
Jun 25, 2020·Briefings in Bioinformatics·Matteo CominFabio Vandin
Sep 6, 2020·Communications Biology·Hans JonssonAnders F Andersson
Sep 19, 2020·Microbiology Resource Announcements·Wisnu Adi WicaksonoGabriele Berg
Sep 10, 2020·Microorganisms·Diana Ayala-MuñozJennifer L Macalady
Sep 29, 2020·Endocrinology and Metabolism·Jang Won SonSunjae Lee
Aug 29, 2020·Microbiology Resource Announcements·Wisnu Adi WicaksonoGabriele Berg
Mar 21, 2020·Microbiology Resource Announcements·Matilde MarquesRodrigo Costa
Aug 14, 2020·MSystems·Kristina BayerBeate M Slaby
Feb 13, 2020·MSystems·Thomas Yssing MichaelsenMads Albertsen
Aug 9, 2020·Nucleic Acids Research·Michael ShafferKelly C Wrighton
Jul 22, 2020·Nature Biotechnology·Alexandre AlmeidaRobert D Finn
Sep 22, 2020·PeerJ·Andres BenavidesFelipe Cabarcas

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Methods Mentioned

BETA
whole genome shotgun sequencing
Hi-C

Software Mentioned

CheckM
COCACOLA
metaSPAdes
cmsearch
MaxBin
BinSanity
SE
MetaBAT
MaxBin2
MetaWatt

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