happi: a hierarchical approach to pangenomics inference

Abstract

AbstractRecovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose , an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation.