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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 empiricaldoi:10.7717/peerj.1165 pmid:26336640 pmcid:PMC4556158 fatcat:odsbsphyvnhbxbjmjhesvjsgyi