SUMMARY

We developed , a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since does not involve estimating many parameters, it can process thousands of genomes within a day. can run on phased or unphased genomic data. We have shown how can be applied to the identification of differentially enriched pathways between populations. The local ancestry approach results in higher enrichment scores compared to whole-genome approaches. We benchmarked PyLAE using the 1000 Genomes dataset, comparing the aggregated predictions with the global admixture results and the current gold standard program RFMix. Computational efficiency, minimal requirements for data pre-processing, straightforward presentation of results, and ease of installation make a valuable tool to study admixed populations.

AVAILABILITY AND IMPLEMENTATION

The source code and installation manual are available at https://github.com/smetam/pylae.