Binning is to cluster similar contigs assembled from reads based on the coverage and sequences composition (e.g., kmer composition) of contigs. The resulting bin, which we also called metagenomic assembled genome (MAG), as a representative of the true collection of species population genome.

The massive amount of metagenomic sequencing has created a challenge: tons of microbial genomes assembled and binned from environmental samples. To compare those genomes (or MAGs) to investigate genomic diversity, average nucleitide identity (or ANI) is the most widely used and reliable way to calculate genome identity. Alignment-based ANI calculators, e.g., OrthoANI or ani.rb (enveomics package) are too slow for a dozens of genomes.