Journal article
The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing
Briefings in Functional Genomics, Vol.18(1), pp.1-12
2019
Abstract
The application of third-generation sequencing (TGS) technology in genetics and genomics have provided opportunities to categorize and explore the individual genomic landscapes and mutations relevant for diagnosis and therapy using whole genome sequencing and de novo genome assembly. In general, the emerging TGS technology can produce high quality long reads for the determination of overlapping reads and transcript isoforms. However, this technology still faces challenges such as the accuracy for the identification of nucleotide bases and high error rates. Here, we surveyed 39 TGS-related tools for de novo assembly and genome analysis to identify the differences among their characteristics, such as the required input, the interaction with the user, sequencing platforms, type of reads, error models, the possibility of introducing coverage bias, the simulation of genomic variants and outputs provided. The decision trees are summarized to help researchers to find out the most suitable tools to analyze the TGS data. Our comprehensive survey and evaluation of computational features of existing methods for TGS may provide a valuable guideline for researchers.
Details
- Title
- The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing
- Authors
- Yong Kiat Wee (Author) - University of the Sunshine Coast, Queensland, School of Science and Engineering - LegacySalma Bhyan (Author) - University of the Sunshine Coast, Queensland, School of Science and Engineering - LegacyYining Liu (Author) - Guangzhou Medical University, ChinaJiachun Lu (Author) - Guangzhou Medical University, ChinaXiaoyan Li (Corresponding Author) - Capital Medical University, ChinaMin Zhao (Corresponding Author) - University of the Sunshine Coast, Queensland, School of Science and Engineering - Legacy
- Publication details
- Briefings in Functional Genomics, Vol.18(1), pp.1-12
- Publisher
- Oxford University Press
- DOI
- 10.1093/bfgp/ely037
- ISSN
- 2041-2649
- Organisation Unit
- GeneCology Research Centre - Legacy; Library Services; Centre for Bioinnovation; School of Science, Technology and Engineering; University of the Sunshine Coast, Queensland; School of Health and Behavioural Sciences - Legacy; School of Science and Engineering - Legacy; School of Health - Biomedicine
- Language
- English
- Record Identifier
- 99450795202621
- Output Type
- Journal article
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- Biotechnology & Applied Microbiology
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