Phased nanopore assembly with Shasta and modular graph phasing with GFAse.

Autor:	Lorig-Roach R; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; rlorigro@ucsc.edu pacarnev@ucsc.edu bpaten@ucsc.edu., Meredith M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Monlong J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Jain M; Department of Bioengineering, Department of Physics, Northeastern University, Boston, Massachusetts 02120, USA., Olsen HE; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., McNulty B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA., Montague TG; The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York 10027, USA.; Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA., Lucas JK; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Condon C; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Eizenga JM; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Juul S; Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA., McKenzie SK; Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA., Simmonds SE; Chan Zuckerberg Initiative Foundation, Redwood City, California 94063, USA., Park J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Asri M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA., Eichler EE; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA., Axel R; The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York 10027, USA.; Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA., Martin B; Chan Zuckerberg Initiative Foundation, Redwood City, California 94063, USA., Carnevali P; Chan Zuckerberg Initiative Foundation, Redwood City, California 94063, USA; rlorigro@ucsc.edu pacarnev@ucsc.edu bpaten@ucsc.edu., Miga KH; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA., Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; rlorigro@ucsc.edu pacarnev@ucsc.edu bpaten@ucsc.edu.
Jazyk:	angličtina
Zdroj:	Genome research [Genome Res] 2024 Apr 25; Vol. 34 (3), pp. 454-468. Date of Electronic Publication: 2024 Apr 25.
DOI:	10.1101/gr.278268.123
Abstrakt:	Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality. (© 2024 Lorig-Roach et al.; Published by Cold Spring Harbor Laboratory Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu