Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes

Abstract

AbstractMetagenomics enables the study of microbial communities and their individual members through shotgun sequencing. An essential phase of metagenomic analysis is the recovery of metagenome-assembled genomes (MAGs). In a metagenomic analysis, sequence reads are assembled into contigs, which are then grouped into bins based on common characteristics - a process known as binning - to generate MAGs. The approach of applying multiple binning methods and combining them in a process called bin refinement allows us to obtain more and higher quality MAGs from metagenomic datasets. We present Binette, a bin refinement tool inspired by metaWRAP’s bin refinement module, which addresses the limitations of the latter and ensures better results. Binette achieves this by creating new hybrid bins using basic set operations from the input bin sets. CheckM2 is then used to assess bin quality and select the best possible bins.