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. This study shows, when analyzing multi-sample metagenomic datasets, the multi-coverage binning approach outperforms the single-coverage binning alternative in generating bins with higher quality and less contamination.

Automated summary

We compared single- and multi-coverage binning on the same set of samples and found that multi-coverage binning outperformed single-coverage binning by identifying contaminant contigs and chimeric bins that other approaches missed. Although resource expensive, multi-coverage binning should always be prioritized as it generates higher quality and less contaminated bins. This study demonstrates the superiority of the multi-coverage binning approach in analyzing multi-sample metagenomic datasets.