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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Bibliographic Details
Published in:	Nature biotechnology Vol. 37; no. 8; pp. 907 - 915
Main Authors:	Kim, Daehwan, Paggi, Joseph M, Park, Chanhee, Bennett, Christopher, Salzberg, Steven L
Format:	Journal Article
Language:	English
Published:	United States Nature Publishing Group 01.08.2019
Subjects:	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
Online Access:	Get full text
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