Dense and accurate whole-chromosome haplotyping of individual genomes

• DOI: 10.1038/s41467-017-01389-4
• Publication Date: 2017-10-30T14:42:34Z
• Authors: David Porubsky; Shilpa Garg; Ashley D. Sanders; Jan O. Korbel; Victor Guryev; Peter M. Lansdorp; Tobias Marschall
• Keywords: Haplotype estimation; 1000 Genomes Project

Abstract The diploid nature of the human genome is neglected in many analyses done today, where a perceived as set unphased variants with respect to reference genome. This lack haplotype-level can be explained by methods that produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy combines global, but sparse obtained from strand-specific single-cell sequencing (Strand-seq) dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on required depths reliably assign more than 95% alleles (NA12878) their parental using few 10 Strand-seq libraries combination 10-fold coverage PacBio data or, alternatively, 10X Genomics data. conclude different technologies represents attractive solution chart genetic variation genomes.