Comparing assembly strategies for third-generation sequencing technologies across different genomes

The recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computat...

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Autores: Espinosa García, Elena, Bautista Moreno, Rocío, Fernández Vega, Ivan, Larrosa Jiménez, Rafael, Lopez Zapata, Emilio, Plata González, Oscar Guillermo
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/395093
Acceso en línea:https://hdl.handle.net/2117/395093
https://dx.doi.org/10.1016/j.ygeno.2023.110700
Access Level:acceso abierto
Palabra clave:Genomics
Sequence alignment (Bioinformatics)
Genome assembly
Hybrid assembly
HiFi
ONT
PacBio
Genòmica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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spelling Comparing assembly strategies for third-generation sequencing technologies across different genomesEspinosa García, ElenaBautista Moreno, RocíoFernández Vega, IvanLarrosa Jiménez, RafaelLopez Zapata, EmilioPlata González, Oscar GuillermoGenomicsSequence alignment (Bioinformatics)Genome assemblyHybrid assemblyHiFiONTPacBioGenòmicaÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaThe recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computational cost and the quality of the results. Accordingly, sequencing accuracy and throughput continue to improve, and many tools are constantly emerging. Therefore, selecting the correct sequencing platform, the proper sequencing depth and the assembly tools are necessary to perform high-quality assembly. This paper evaluates the primary assembly reconstruction from recent hybrid and non-hybrid pipelines on different genomes. We find that using PacBio high-fidelity long-read (HiFi) plays an essential role in haplotype construction with respect to ONT reads. However, we observe a substantial improvement in the correctness of the assembly from high-fidelity ONT datasets and combining it with HiFi or short-reads.This work has been partially supported by the Spanish MINECO PID2019-105396RB-I00, Junta de Andalucia JA2018 P18-FR-3433, and UMA18-FEDERJA-197 projects. Funding for open access charge: Universidad de Málaga/CBUA.Peer ReviewedElsevier20232023-09-0120232023-10-19journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/395093https://dx.doi.org/10.1016/j.ygeno.2023.110700reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3950932026-05-27T15:37:01Z
dc.title.none.fl_str_mv Comparing assembly strategies for third-generation sequencing technologies across different genomes
title Comparing assembly strategies for third-generation sequencing technologies across different genomes
spellingShingle Comparing assembly strategies for third-generation sequencing technologies across different genomes
Espinosa García, Elena
Genomics
Sequence alignment (Bioinformatics)
Genome assembly
Hybrid assembly
HiFi
ONT
PacBio
Genòmica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
title_short Comparing assembly strategies for third-generation sequencing technologies across different genomes
title_full Comparing assembly strategies for third-generation sequencing technologies across different genomes
title_fullStr Comparing assembly strategies for third-generation sequencing technologies across different genomes
title_full_unstemmed Comparing assembly strategies for third-generation sequencing technologies across different genomes
title_sort Comparing assembly strategies for third-generation sequencing technologies across different genomes
dc.creator.none.fl_str_mv Espinosa García, Elena
Bautista Moreno, Rocío
Fernández Vega, Ivan
Larrosa Jiménez, Rafael
Lopez Zapata, Emilio
Plata González, Oscar Guillermo
author Espinosa García, Elena
author_facet Espinosa García, Elena
Bautista Moreno, Rocío
Fernández Vega, Ivan
Larrosa Jiménez, Rafael
Lopez Zapata, Emilio
Plata González, Oscar Guillermo
author_role author
author2 Bautista Moreno, Rocío
Fernández Vega, Ivan
Larrosa Jiménez, Rafael
Lopez Zapata, Emilio
Plata González, Oscar Guillermo
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Genomics
Sequence alignment (Bioinformatics)
Genome assembly
Hybrid assembly
HiFi
ONT
PacBio
Genòmica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
topic Genomics
Sequence alignment (Bioinformatics)
Genome assembly
Hybrid assembly
HiFi
ONT
PacBio
Genòmica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
description The recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computational cost and the quality of the results. Accordingly, sequencing accuracy and throughput continue to improve, and many tools are constantly emerging. Therefore, selecting the correct sequencing platform, the proper sequencing depth and the assembly tools are necessary to perform high-quality assembly. This paper evaluates the primary assembly reconstruction from recent hybrid and non-hybrid pipelines on different genomes. We find that using PacBio high-fidelity long-read (HiFi) plays an essential role in haplotype construction with respect to ONT reads. However, we observe a substantial improvement in the correctness of the assembly from high-fidelity ONT datasets and combining it with HiFi or short-reads.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-09-01
2023
2023-10-19
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/395093
https://dx.doi.org/10.1016/j.ygeno.2023.110700
url https://hdl.handle.net/2117/395093
https://dx.doi.org/10.1016/j.ygeno.2023.110700
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300724

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