Du, Z.-Z. | bioRxiv Science

bioRxiv2025

Varigraph: an accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes

Graph pangenome references can address single-reference bias, thereby enhancing the accuracy of variant genotyping and empowering downstream applications in population genetics and quantitative genetics. However, existing pangenome-based genotyping methods struggle with large or complex pangenome graphs, particularly in polyploid genomes. Here, we introduce Varigraph, an algorithm that leverages the comparison of unique and repetitive k-mers between variant sites and short reads for genotyping both small and large variants. Varigraph outperforms current state-of-the-art linear and graph-based genotypers across non-human genomes while maintaining comparable accuracy in human genomes. By employing an efficient data structure, Varigraph achieves higher accuracy in repetitive regions while managing computational costs for large datasets. Notably, Varigraph is the first tool capable of effectively utilizing pangenome graphs for genotyping autopolyploids, enabling precise determination of allele dosage. This work provides a robust and accurate solution for genotyping non-human genomes and will facilitate genomic studies of polyploid crops.

genomics↗

bioRxiv2023

A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline

BackgroundAlthough sequencing technologies have boosted the measurement of the sequencing diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods have been developed to address this issue and tested for human genomes, however, their performance in plant genomes remains largely elusive. Furthermore, pipelines integrating the advantages of current genotyping methods might be required, considering the different complexity of plant genomes. ResultsHere we comprehensively evaluate eight such genotypers in different scenarios in terms of variant type and size, sequencing parameters, genomic context, and complexity, as well as graph size, using both simulated and read data sets from representative plant genomes. Our evaluation reveals that there are still great challenges to applying existing methods to plants, such as excessive repeats and variants or high resource consumption. Therefore, we propose a pipeline called Ensemble Variant Genotyper (EVG) that can achieve better genotype concordances without increasing resource consumption. EVG can achieve comparably higher genotyping recall and precision even using 5x reads. Furthermore, we demonstrate that EVG is more robust with an increasing number of variants, especially for insertion and deletion. ConclusionsOur study will provide new insights into the development and application of graph-based genotyping algorithms. We conclude that EVG provides an accurate, unbiased, and cost-effective way for genotyping both small and large variations and will be potentially used in population-scale genotyping for large, repetitive, and heterozygous plant genomes.

genomics↗