Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Abstract

As a step towards simplifying and reducing the cost of haplotype resolved <i>de novo</i> 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.