Phased nanopore assembly with Shasta and modular graph phasing with GFAse

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 Oxfor...

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Autores principales: Lorig-Roach, Ryan, Meredith, Melissa, Monlong, Jean, Jain, Miten, Olsen, Hugh, McNulty, Brandy, Porubsky, David, Montague, Tessa, Lucas, Julian, Condon, Chris, Eizenga, Jordan, Juul, Sissel, McKenzie, Sean, Simmonds, Sara E., Park, Jimin, Asri, Mobin, Koren, Sergey, Eichler, Evan, Axel, Richard, Martin, Bruce, Carnevali, Paolo, Miga, Karen, Paten, Benedict
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980101/
https://www.ncbi.nlm.nih.gov/pubmed/36865218
http://dx.doi.org/10.1101/2023.02.21.529152
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author Lorig-Roach, Ryan
Meredith, Melissa
Monlong, Jean
Jain, Miten
Olsen, Hugh
McNulty, Brandy
Porubsky, David
Montague, Tessa
Lucas, Julian
Condon, Chris
Eizenga, Jordan
Juul, Sissel
McKenzie, Sean
Simmonds, Sara E.
Park, Jimin
Asri, Mobin
Koren, Sergey
Eichler, Evan
Axel, Richard
Martin, Bruce
Carnevali, Paolo
Miga, Karen
Paten, Benedict
author_facet Lorig-Roach, Ryan
Meredith, Melissa
Monlong, Jean
Jain, Miten
Olsen, Hugh
McNulty, Brandy
Porubsky, David
Montague, Tessa
Lucas, Julian
Condon, Chris
Eizenga, Jordan
Juul, Sissel
McKenzie, Sean
Simmonds, Sara E.
Park, Jimin
Asri, Mobin
Koren, Sergey
Eichler, Evan
Axel, Richard
Martin, Bruce
Carnevali, Paolo
Miga, Karen
Paten, Benedict
author_sort Lorig-Roach, Ryan
collection PubMed
description 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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spelling pubmed-99801012023-03-03 Phased nanopore assembly with Shasta and modular graph phasing with GFAse Lorig-Roach, Ryan Meredith, Melissa Monlong, Jean Jain, Miten Olsen, Hugh McNulty, Brandy Porubsky, David Montague, Tessa Lucas, Julian Condon, Chris Eizenga, Jordan Juul, Sissel McKenzie, Sean Simmonds, Sara E. Park, Jimin Asri, Mobin Koren, Sergey Eichler, Evan Axel, Richard Martin, Bruce Carnevali, Paolo Miga, Karen Paten, Benedict bioRxiv Article 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. Cold Spring Harbor Laboratory 2023-02-22 /pmc/articles/PMC9980101/ /pubmed/36865218 http://dx.doi.org/10.1101/2023.02.21.529152 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Lorig-Roach, Ryan
Meredith, Melissa
Monlong, Jean
Jain, Miten
Olsen, Hugh
McNulty, Brandy
Porubsky, David
Montague, Tessa
Lucas, Julian
Condon, Chris
Eizenga, Jordan
Juul, Sissel
McKenzie, Sean
Simmonds, Sara E.
Park, Jimin
Asri, Mobin
Koren, Sergey
Eichler, Evan
Axel, Richard
Martin, Bruce
Carnevali, Paolo
Miga, Karen
Paten, Benedict
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
title Phased nanopore assembly with Shasta and modular graph phasing with GFAse
title_full Phased nanopore assembly with Shasta and modular graph phasing with GFAse
title_fullStr Phased nanopore assembly with Shasta and modular graph phasing with GFAse
title_full_unstemmed Phased nanopore assembly with Shasta and modular graph phasing with GFAse
title_short Phased nanopore assembly with Shasta and modular graph phasing with GFAse
title_sort phased nanopore assembly with shasta and modular graph phasing with gfase
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980101/
https://www.ncbi.nlm.nih.gov/pubmed/36865218
http://dx.doi.org/10.1101/2023.02.21.529152
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