Benchmarks for various binning methods.

24 samples from the Pasolli et al study were run through the PATRIC binning tool, MetaBAT2 with depth files generated from the original FASTQ reads using Bowtie2, and MetaBAT2 on raw contigs. These bins were compared to the results generated in the Pasolli et al study via a custom pipeline which also used Bowtie2 and MetaBAT2. Each studied group splits found bins into “good” bins, i.e. those matching the PATRIC criteria for a high-quality bin, and “poor” quality bins which do not meet the criteria. In general, PATRIC found more high-quality bins than MetaBAT2 with or without alignment, although theoretically better MetaBAT2 performance is demonstrated via the Pasolli et al study. The PATRIC binning tool found substantially fewer poor-quality bins than any of the other binning methods.