Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies

High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental desi...

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Autores principales:	John M. Sutton, Joshua D. Millwood, A. Case McCormack, Janna L. Fierst
Formato:	article
Lenguaje:	EN
Publicado:	GigaScience Press 2021
Materias:	Electronic computers. Computer science QA75.5-76.95
Acceso en línea:	https://doaj.org/article/d03590348743469fb6e45b806edc6948
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spelling	oai:doaj.org-article:d03590348743469fb6e45b806edc69482021-12-02T18:32:52ZOptimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies10.46471/gigabyte.272709-4715https://doaj.org/article/d03590348743469fb6e45b806edc69482021-07-01T00:00:00Zhttps://gigabytejournal.com/articles/27https://doaj.org/toc/2709-4715 High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms. Here, we present novel results using simulated and empirical ONT and DNA libraries to identify best practices for sequencing and assembly for several model species. We find that the unique error structure of ONT libraries causes errors to accumulate and assembly statistics plateau as sequence depth increases. High-quality assembled eukaryotic sequences require high-molecular-weight DNA extractions that increase sequence read length, and computational protocols that reduce error through pre-assembly correction and read selection. Our quantitative results will be helpful for researchers seeking guidance for de novo assembly projects. John M. SuttonJoshua D. MillwoodA. Case McCormackJanna L. FierstGigaScience PressarticleElectronic computers. Computer scienceQA75.5-76.95ENGigaByte (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Electronic computers. Computer science QA75.5-76.95
spellingShingle	Electronic computers. Computer science QA75.5-76.95 John M. Sutton Joshua D. Millwood A. Case McCormack Janna L. Fierst Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
description	High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms. Here, we present novel results using simulated and empirical ONT and DNA libraries to identify best practices for sequencing and assembly for several model species. We find that the unique error structure of ONT libraries causes errors to accumulate and assembly statistics plateau as sequence depth increases. High-quality assembled eukaryotic sequences require high-molecular-weight DNA extractions that increase sequence read length, and computational protocols that reduce error through pre-assembly correction and read selection. Our quantitative results will be helpful for researchers seeking guidance for de novo assembly projects.
format	article
author	John M. Sutton Joshua D. Millwood A. Case McCormack Janna L. Fierst
author_facet	John M. Sutton Joshua D. Millwood A. Case McCormack Janna L. Fierst
author_sort	John M. Sutton
title	Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
title_short	Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
title_full	Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
title_fullStr	Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
title_full_unstemmed	Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
title_sort	optimizing experimental design for genome sequencing and assembly with oxford nanopore technologies
publisher	GigaScience Press
publishDate	2021
url	https://doaj.org/article/d03590348743469fb6e45b806edc6948
work_keys_str_mv	AT johnmsutton optimizingexperimentaldesignforgenomesequencingandassemblywithoxfordnanoporetechnologies AT joshuadmillwood optimizingexperimentaldesignforgenomesequencingandassemblywithoxfordnanoporetechnologies AT acasemccormack optimizingexperimentaldesignforgenomesequencingandassemblywithoxfordnanoporetechnologies AT jannalfierst optimizingexperimentaldesignforgenomesequencingandassemblywithoxfordnanoporetechnologies
_version_	1718377947029569536

Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies

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