@article{Lorig-Roach01032024,
author = {Lorig-Roach, Ryan and Meredith, Melissa and Monlong, Jean and Jain, Miten and Olsen, Hugh E. and McNulty, Brandy and Porubsky, David and Montague, Tessa G. and Lucas, Julian K. and Condon, Chris and Eizenga, Jordan M. and Juul, Sissel and McKenzie, Sean K. and Simmonds, Sara E. and Park, Jimin and Asri, Mobin and Koren, Sergey and Eichler, Evan E. and Axel, Richard and Martin, Bruce and Carnevali, Paolo and Miga, Karen H. and Paten, Benedict}, 
title = {Phased nanopore assembly with Shasta and modular graph phasing with GFAse},
volume = {34}, 
number = {3}, 
pages = {454-468}, 
year = {2024}, 
doi = {10.1101/gr.278268.123}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/34/3/454.abstract}, 
eprint = {http://genome.cshlp.org/content/34/3/454.full.pdf+html}, 
journal = {Genome Research} 
}