Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

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 us...

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Vydáno v:Nature biotechnology Ročník 37; číslo 8; s. 907 - 915
Hlavní autoři: Kim, Daehwan, Paggi, Joseph M, Park, Chanhee, Bennett, Christopher, Salzberg, Steven L
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Nature Publishing Group 01.08.2019
Témata:
Alignment
Base Sequence
Benchmarking
Computer applications
Computer simulation
Data structures
Deoxyribonucleic acid
DNA
DNA fingerprinting
Gene sequencing
Genetic fingerprinting
Genetic Variation
Genome, Human
Genomes
Genomics
Genotype
Genotype & phenotype
Genotypes
Genotyping
Haplotypes
Histocompatibility antigen HLA
Humans
Nucleotide sequence
Reproducibility of Results
Ribonucleic acid
RNA
Search algorithms
Sequence Analysis, DNA - methods
Sequence Analysis, RNA - methods
Software
Tissue typing
ISSN:1087-0156, 1546-1696, 1546-1696
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Popis
Shrnutí: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.
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ISSN:1087-0156
1546-1696
1546-1696
DOI:10.1038/s41587-019-0201-4