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

PeerJ. 2019 Jul 26;7:e7359. doi: 10.7717/peerj.7359. eCollection 2019.


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 at

Keywords: Clustering; Metagenome binning; Metagenomics.

Grant support

Dongwan Kang, Edward Kirton, Ashleigh Thomas, Rob Egan, and Zhong Wang’s work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Feng Li was supported by an exchange student fellowship from the China Scholarship Council (CSC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.