Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Lorig-Roach Ryan and Meredith Melissa and Monlong Jean and Jain Miten and Olsen Hugh and McNulty Brandy and Porubsky David and Montague Tessa and Lucas Julian and Condon Chris and Eizenga Jordan and Juul Sissel and McKenzie Sean and Simmonds

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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February, 2023



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