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| Item Type: | Preprint |
|---|---|
| Title: | A fully phased accurate assembly of an individual human genome |
| Creators Name: | Porubsky, D., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Munson, K.M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P.M., Paten, B., Devine, S.E., Sanders, A.D., Lee, C., Chaisson, M.J.P., Korbel, J.O., Eichler, E.E. and Marschall, T. |
| Abstract: | The prevailing genome assembly paradigm is to produce consensus sequences that "collapse" parental haplotypes into a consensus sequence. Here, we leverage the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing (Strand-seq) and combine them with high-fidelity (HiFi) long sequencing reads, in a novel reference-free workflow for diploid de novo genome assembly. Employing this strategy, we produce completely phased de novo genome assemblies separately for each haplotype of a single individual of Puerto Rican origin (HG00733) in the absence of parental data. The assemblies are accurate (QV > 40), highly contiguous (contig N50 > 25 Mbp) with low switch error rates (0.4%) providing fully phased single-nucleotide variants (SNVs), indels, and structural variants (SVs). A comparison of Oxford Nanopore and PacBio phased assemblies identifies 150 regions that are preferential sites of contig breaks irrespective of sequencing technology or phasing algorithms. |
| Keywords: | Genome Assembly, Phasing, Structural Variation, Diploid Genome, Long-Read Sequencing, Strand-Seq |
| Source: | bioRxiv |
| Title of Book: | A fully phased accurate assembly of an individual human genome |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Article Number: | 855049 |
| Date: | 26 November 2019 |
| Official Publication: | https://doi.org/10.1101/855049 |
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