Hmmibd-rs: an enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale Plasmodium genomic data.

ABSTRACT:

Background

Identity-by-descent (IBD), which describes recent genetic co-ancestry between pairs of genomes, is a fundamental concept in population genomics. It has been used to estimate genetic relatedness, detect selection signals, and understand population demography. The IBD detection method hmmIBD demonstrates high accuracy in inferring IBD segments between haploid genomes, including Plasmodium falciparum, and is widely used in malaria genomic surveillance. However, the current single-threaded implementation of hmmIBD does not utilize the full capacity of multi-processor computers, making it difficult to apply to large data sets, and does not accommodate non-uniform recombination rates across the genome.

Methods

We developed an enhanced implementation of hmmIBD, named hmm

SUBMITTER: Guo B 

PROVIDER: S-EPMC12922355 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature