A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination.

Metagenomic binning has revolutionized the study of uncultured microorganisms. Here we compare single- and multi-coverage binning on the same set of samples, and demonstrate that multi-coverage binning produces better results than single-coverage binning and identifies contaminant contigs and chimeric bins that other approaches miss. While resource expensive, multi-coverage binning is a superior approach and should always be performed over single-coverage binning.