Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Ryan Lorig-Roach; Melissa Meredith; Jean Monlong; Miten Jain; Hugh E. Olsen; Brandy McNulty; David Porubskỳ; Tessa G. Montague; Julian Lucas; Chris Condon; Jordan M. Eizenga; Sissel Juul; Sean K. McKenzie; Sara E. Simmonds; Jimin Park; Mobin Asri; Sergey Koren; Evan E. Eichler; Richard Axel; Bruce Martin; Paolo Carnevali; Karen H. Miga; Benedict Paten

doi:10.1101/gr.278268.123

BioinformaticsGenome ResearchApr 16, 2024

Peer-reviewed journal article

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Ryan Lorig-Roach iD, Melissa Meredith iD, Jean Monlong iD, Miten Jain iD, Hugh E. Olsen iD, Brandy McNulty, David Porubskỳ iD, Tessa G. Montague iD, Julian Lucas iD, Chris Condon, Jordan M. Eizenga iD, Sissel Juul iD, Sean K. McKenzie iD, Sara E. Simmonds iD, Jimin Park iD, Mobin Asri iD, Sergey Koren iD, Evan E. Eichler iD, Richard Axel iD, Bruce Martin, Paolo Carnevali, Karen H. Miga iD, Benedict Paten iD

Abstract

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.

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