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, CA, USA., Meredith M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Monlong J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Jain M; Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA., Olsen H; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., McNulty B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Montague T; The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY, USA & Howard Hughes Medical Institute, Columbia University, New York, NY, USA., Lucas J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Condon C; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Eizenga J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Juul S; Oxford Nanopore Technologies Inc., McKenzie S; Oxford Nanopore Technologies Inc., Simmonds SE; Chan Zuckerberg Initiative Foundation, Redwood City, CA, USA., Park J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Asri M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome & Research Institute, National Institutes of Health, Bethesda, MD USA., Eichler E; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA & Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Axel R; The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY, USA & Howard Hughes Medical Institute, Columbia University, New York, NY, USA., Martin B; Chan Zuckerberg Initiative Foundation, Redwood City, CA, USA., Carnevali P; Chan Zuckerberg Initiative Foundation, Redwood City, CA, USA., Miga K; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Jazyk: angličtina
Zdroj: BioRxiv : the preprint server for biology [bioRxiv] 2023 Feb 22. Date of Electronic Publication: 2023 Feb 22.
DOI: 10.1101/2023.02.21.529152
Abstrakt: As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore 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 Oxford Nanopore Technologies' (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.
Databáze: MEDLINE