RT Journal
A1 Lorig-Roach, Ryan
A1 Meredith, Melissa
A1 Monlong, Jean
A1 Jain, Miten
A1 Olsen, Hugh E.
A1 McNulty, Brandy
A1 Porubsky, David
A1 Montague, Tessa G.
A1 Lucas, Julian K.
A1 Condon, Chris
A1 Eizenga, Jordan M.
A1 Juul, Sissel
A1 McKenzie, Sean K.
A1 Simmonds, Sara E.
A1 Park, Jimin
A1 Asri, Mobin
A1 Koren, Sergey
A1 Eichler, Evan E.
A1 Axel, Richard
A1 Martin, Bruce
A1 Carnevali, Paolo
A1 Miga, Karen H.
A1 Paten, Benedict
T1 Phased nanopore assembly with Shasta and modular graph phasing with GFAse
JF Genome Research 
JO Genome Research 
YR 2024 
FD March 01 
VO 34 
IS 3 
SP 454 
OP 468 
DO 10.1101/gr.278268.123 
UL http://genome.cshlp.org/content/34/3/454.abstract 
AB Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence 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 ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality.