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hmmibd-rs: An enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale
Bing Guo1, Stephen F Schaffner2, Aimee R Taylor3
1University of Maryland School of Medicine.
Research Square
|July 9, 2025
Summary
A new Rust implementation, hmmibd-rs, accelerates identity-by-descent (IBD) detection by 100x using multi-threading and improves accuracy with non-uniform recombination rates. This tool enhances large-scale malaria genomic surveillance capabilities.
Area of Science:
- Population Genomics
- Computational Biology
- Genomic Surveillance
Background:
- Identity-by-descent (IBD) is crucial for understanding genetic relatedness, selection, and population demography.
- The hmmIBD tool accurately infers IBD segments in haploid genomes, widely used for malaria genomic surveillance.
- Existing hmmIBD implementation is single-threaded and does not account for non-uniform recombination rates, limiting scalability.
Purpose of the Study:
- To develop an enhanced, multi-threaded implementation of hmmIBD for faster and more accurate IBD detection.
- To incorporate support for non-uniform recombination rates to improve IBD inference accuracy.
- To streamline large-scale IBD detection from raw genomic data.
Main Methods:
- Developed hmmibd-rs, a multi-threaded implementation in Rust, parallelizing IBD inference across genome pairs.
- Integrated support for user-defined recombination rate maps to handle genomic non-uniformity.
- Added functionalities for direct input preprocessing from BCF format and output filtering for reduced disk usage.
Main Results:
- hmmibd-rs achieves near-linear speedup with increased CPU threads, reducing computation time by approximately 100x for large simulated datasets.
- Accounting for non-uniform recombination rates improves IBD inference accuracy, reducing false positives in cold spots and false negatives in hot spots.
- Analysis of the MalariaGEN Pf7 dataset (approx. 10,000 samples) completed within hours, enabling a single-day IBD analysis pipeline.
Conclusions:
- hmmibd-rs significantly accelerates and enhances IBD detection compared to the original hmmIBD.
- The tool provides efficient and accurate IBD detection, crucial for large-scale genomic analyses.
- It serves as a vital tool for advancing malaria genomic surveillance.
