Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-08-02

AUTHORS

Daehwan Kim, Joseph M. Paggi, Chanhee Park, Christopher Bennett, Steven L. Salzberg

ABSTRACT

The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. We use HISAT2 to represent and search an expanded model of the human reference genome in which over 14.5 million genomic variants in combination with haplotypes are incorporated into the data structure used for searching and alignment. We benchmark HISAT2 using simulated and real datasets to demonstrate that our strategy of representing a population of genomes, together with a fast, memory-efficient search algorithm, provides more detailed and accurate variant analyses than other methods. We apply HISAT2 for HLA typing and DNA fingerprinting; both applications form part of the HISAT-genotype software that enables analysis of haplotype-resolved genes or genomic regions. HISAT-genotype outperforms other computational methods and matches or exceeds the performance of laboratory-based assays. More... »

PAGES

907-915

References to SciGraph publications

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  • 2015-03-09. HISAT: a fast spliced aligner with low memory requirements in NATURE METHODS
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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41587-019-0201-4

    DOI

    http://dx.doi.org/10.1038/s41587-019-0201-4

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1120026584

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31375807


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