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doi:10.22028/D291-28721
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 |
Publisher/Platform: | Nature Publishing Group UK |
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 |
URL of the first publication: | https://www.nature.com/articles/s41467-017-01389-4 |
Link to this record: | hdl:20.500.11880/27715 http://dx.doi.org/10.22028/D291-28721 |
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: | SciDok - Der Wissenschaftsserver der Universität des Saarlandes |
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