RT Journal Article
SR Electronic
T1 happi: a Hierarchical Approach to Pangenomics Inference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.04.26.489591
DO 10.1101/2022.04.26.489591
A1 Pauline Trinh
A1 David S. Clausen
A1 Amy D. Willis
YR 2022
UL http://biorxiv.org/content/early/2022/04/28/2022.04.26.489591.abstract
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.