A fully phased accurate assembly of an individual human genome
| Item Type: | Preprint |
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| Title: | A fully phased accurate assembly of an individual human genome |
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| Creators Name: | Porubsky, D. and Ebert, P. and Audano, P.A. and Vollger, M.R. and Harvey, W.T. and Munson, K.M. and Sorensen, M. and Sulovari, A. and Haukness, M. and Ghareghani, M. and Lansdorp, P.M. and Paten, B. and Devine, S.E. and Sanders, A.D. and Lee, C. and Chaisson, M.J.P. and Korbel, J.O. and Eichler, E.E. and Marschall, T. |
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| 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. |
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| Keywords: | Genome Assembly, Phasing, Structural Variation, Diploid Genome, Long-Read Sequencing, Strand-Seq |
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| Source: | bioRxiv |
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| Title of Book: | A fully phased accurate assembly of an individual human genome |
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| Publisher: | Cold Spring Harbor Laboratory Press |
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| Article Number: | 855049 |
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| Date: | 26 November 2019 |
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| Official Publication: | https://doi.org/10.1101/855049 |
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