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bioRxiv · 10.1101/266197

HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer

Kim, D.·Paggi, J. M.·Salzberg, S.
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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 HISAT-genotypes accuracy 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.\n\nOne Sentence SummaryHISAT-genotype is a software platform that has the ability to genotype all the genes in an individuals genome within a few hours on a desktop computer.

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Kim, D., Paggi, J. M., Salzberg, S.. 2018-02-15. HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer. https://doi.org/10.1101/266197

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