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Twelve quick steps for genome assembly and annotation in the classroom

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing ex...

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Autores principales: Jung, Hyungtaek, Ventura, Tomer, Chung, J. Sook, Kim, Woo-Jin, Nam, Bo-Hye, Kong, Hee Jeong, Kim, Young-Ok, Jeon, Min-Seung, Eyun, Seong-il
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660529/
https://www.ncbi.nlm.nih.gov/pubmed/33180771
http://dx.doi.org/10.1371/journal.pcbi.1008325
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author Jung, Hyungtaek
Ventura, Tomer
Chung, J. Sook
Kim, Woo-Jin
Nam, Bo-Hye
Kong, Hee Jeong
Kim, Young-Ok
Jeon, Min-Seung
Eyun, Seong-il
author_facet Jung, Hyungtaek
Ventura, Tomer
Chung, J. Sook
Kim, Woo-Jin
Nam, Bo-Hye
Kong, Hee Jeong
Kim, Young-Ok
Jeon, Min-Seung
Eyun, Seong-il
author_sort Jung, Hyungtaek
collection PubMed
description Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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spelling pubmed-76605292020-11-18 Twelve quick steps for genome assembly and annotation in the classroom Jung, Hyungtaek Ventura, Tomer Chung, J. Sook Kim, Woo-Jin Nam, Bo-Hye Kong, Hee Jeong Kim, Young-Ok Jeon, Min-Seung Eyun, Seong-il PLoS Comput Biol Education Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community. Public Library of Science 2020-11-12 /pmc/articles/PMC7660529/ /pubmed/33180771 http://dx.doi.org/10.1371/journal.pcbi.1008325 Text en © 2020 Jung et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Education
Jung, Hyungtaek
Ventura, Tomer
Chung, J. Sook
Kim, Woo-Jin
Nam, Bo-Hye
Kong, Hee Jeong
Kim, Young-Ok
Jeon, Min-Seung
Eyun, Seong-il
Twelve quick steps for genome assembly and annotation in the classroom
title Twelve quick steps for genome assembly and annotation in the classroom
title_full Twelve quick steps for genome assembly and annotation in the classroom
title_fullStr Twelve quick steps for genome assembly and annotation in the classroom
title_full_unstemmed Twelve quick steps for genome assembly and annotation in the classroom
title_short Twelve quick steps for genome assembly and annotation in the classroom
title_sort twelve quick steps for genome assembly and annotation in the classroom
topic Education
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660529/
https://www.ncbi.nlm.nih.gov/pubmed/33180771
http://dx.doi.org/10.1371/journal.pcbi.1008325
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