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Porubsky, David; Ebert, Peter; Audano, Peter A; Vollger, Mitchell R; Harvey, William T; Marijon, Pierre; Ebler, Jana; Munson, Katherine M; Sorensen, Melanie; Sulovari, Arvis; Haukness, Marina; Ghareghani, Maryam; Lansdorp, Peter M; Paten, Benedict; Devine, Scott E; Sanders, Ashley D; Lee, Charles; Chaisson, Mark J P; Korbel, Jan O; Eichler, Evan E; Marschall, Tobias
Nature biotechnology, 03/2021, Letnik: 39, Številka: 3Journal Article
Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing with continuous long-read or high-fidelity sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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in: SICRIS
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