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Abstract
Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses of human genomes. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT-genotype, for representing and searching an expanded model of the human reference genome, in which a comprehensive catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a very fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate the accuracy of HISAT-genotype for HLA typing, a critical task in human organ transplantation, and for the DNA fingerprinting tests widely used in forensics. In both applications, HISAT-genotype not only improves upon earlier computational methods, but matches or exceeds the accuracy of laboratory-based assays.
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