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.

Details

Title
HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer
Author
Kim, Daehwan; Paggi, Joseph M; Salzberg, Steven
University/institution
Cold Spring Harbor Laboratory Press
Section
New Results
Publication year
2018
Publication date
Feb 15, 2018
Publisher
Cold Spring Harbor Laboratory Press
ISSN
2692-8205
Source type
Working Paper
Language of publication
English
ProQuest document ID
2071172224
Copyright
�� 2018. This article is published under http://creativecommons.org/licenses/by/4.0/ (���the License���). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.