Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in High-Recombining <i>Plasmodium falciparum</i> Genomes.

ABSTRACT: Genomic surveillance is crucial for identifying at-risk populations for targeted malaria control and elimination. Identity-by-descent (IBD) is increasingly being used in Plasmodium population genomics to estimate genetic relatedness, effective population size (N _e ), population structure, and signals of positive selection. Despite its potential, a thorough evaluation of IBD segment detection tools for species with high recombination rates, such as P. falciparum, remains absent. Here, we perform comprehensive benchmarking of IBD callers - probabilistic (hmmIBD, isoRelate), identity-by-state-based (hap-IBD, phased IBD) and others (Refined IBD) - using population genetic simulations tailored for high recombination, and IBD quality metrics at both the IBD

SUBMITTER: Guo B 

PROVIDER: S-EPMC11092787 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature