Please use this identifier to cite or link to this item: doi:10.22028/D291-28721
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Title: Dense and accurate whole-chromosome haplotyping of individual genomes
Author(s): Porubsky, David
Garg, Shilpa
Sanders, Ashley D.
Korbel, Jan O.
Guryev, Victor
Lansdorp, Peter M.
Marschall, Tobias
Language: English
Title: Nature communications
Volume: 8
Issue: 1
Startpage: 1293
Publisher/Platform: Nature Publishing Group
Year of Publication: 2017
Publikation type: Journal Article
Abstract: The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on the required sequencing depths and reliably assign more than 95% of alleles (NA12878) to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. We conclude that the combination of Strand-seq with different technologies represents an attractive solution to chart the genetic variation of diploid genomes.
DOI of the first publication: 10.1038/s41467-017-01389-4
Link to this record: hdl:20.500.11880/27715
ISSN: 2041-1723
Date of registration: 7-Sep-2019
Faculty: MI - Fakultät für Mathematik und Informatik
Department: MI - Informatik
Professorship: MI - Prof. Dr. Tobias Marschall
Collections:UniBib – Die Universitätsbibliographie

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