PT  - JOURNAL ARTICLE
AU  - Pauline Trinh
AU  - David S. Clausen
AU  - Amy D. Willis
TI  - happi: a Hierarchical Approach to Pangenomics Inference
AID  - 10.1101/2022.04.26.489591
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.04.26.489591
4099  - http://biorxiv.org/content/early/2022/04/28/2022.04.26.489591.short
4100  - http://biorxiv.org/content/early/2022/04/28/2022.04.26.489591.full
AB  - Recovering 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 happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs and via simulation.Competing Interest StatementThe authors have declared no competing interest.