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Published VersionCC BY V4.0, Open Access
Journal article
Twelve quick steps for genome assembly and annotation in the classroom
PLoS Computational Biology, Vol.16(11), pp.1-25
2020
Abstract
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.
Details
- Title
- Twelve quick steps for genome assembly and annotation in the classroom
- Authors
- Hyungtaek Jung (Author) - The University of QueenslandTomer Ventura (Author) - University of the Sunshine Coast, Queensland, School of Science and Engineering - LegacyJ. Sook Chung (Author) - University of Maryland Center for Environmental ScienceWoo-Jin Kim (Author) - National Institute of Fisheries ScienceBo-Hye Nam (Author) - National Institute of Fisheries ScienceHee Jeong Kong (Author) - National Institute of Fisheries ScienceYoung-Ok Kim (Author) - National Institute of Fisheries ScienceMin-Seung Jeon (Author) - Chung-Ang UniversitySeong-il Eyun (Author) - Chung-Ang University
- Publication details
- PLoS Computational Biology, Vol.16(11), pp.1-25
- Publisher
- Public Library of Science
- Date published
- 2020
- DOI
- 10.1371/journal.pcbi.1008325
- ISSN
- 1553-7358; 1553-734X
- Copyright note
- Copyright (c) 2020 Jung et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- Organisation Unit
- School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99489107302621
- Output Type
- Journal article
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