GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes.

ABSTRACT:

Background

Helicobacter pylori is a highly diverse gastric bacterium whose genomic variation both reflects human migration and complicates genome-wide association studies (GWAS). Its 1.67 Mb genome contains ~ 143,000 biallelic SNPs with minor allele frequency > 1%, making population stratification a major confounder. Existing model- and distance-based methods for bacterial ancestry classification often yield inconsistent results depending on dataset composition. A robust and generalizable framework is needed to improve downstream analyses.

Results

We developed GrafGen, an open-source R package adapted from the human ancestry tool GrafPop, for the classification of H. pylori and prophage populations. Using reference data from the H. pylori Genome Project (1,011 genomes from 5

SUBMITTER: Wheeler W 

PROVIDER: S-EPMC12751694 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature