This pipeline implements competitive fragment recruitment to map metagenomic sequence space against a representative reference genome. In microbial ecology, read recruitment provides a quantitative window into the evolutionary dynamics of natural populations by measuring nucleotide-level polymorphism and consensus sequence divergence.

A genome-resolved metagenomics pipeline replicating the Sharon et al. (2019) gut-brain axis study. Features MEGAHIT de novo co-assembly, Bowtie2 competitive read recruitment, and Anvi'o single-nucleotide variant (SNV) microdiversity profiling.