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.
