The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing

Yong Kiat Wee; Salma Bhyan; Yining Liu; Jiachun Lu; Xiaoyan Li; Min Zhao

doi:10.1093/bfgp/ely037

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The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing

Journal article

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The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing

Yong Kiat Wee, Salma Bhyan, Yining Liu, Jiachun Lu, Xiaoyan Li and Min Zhao

Briefings in Functional Genomics, Vol.18(1), pp.1-12

2019

DOI: https://doi.org/10.1093/bfgp/ely037

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Abstract

third-generation sequencing

genome assembly

mapping

genome sequencing

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 - Legacy
Salma Bhyan (Author) - University of the Sunshine Coast, Queensland, School of Science and Engineering - Legacy
Yining Liu (Author) - Guangzhou Medical University, China
Jiachun Lu (Author) - Guangzhou Medical University, China
Xiaoyan Li (Corresponding Author) - Capital Medical University, China
Min 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
Date published: 2019
DOI: 10.1093/bfgp/ely037
ISSN: 2041-2649
Organisation Unit: School of Health - Biomedicine; School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; Library Services; School of Science, Technology and Engineering; Centre for Bioinnovation; School of Health and Behavioural Sciences - Legacy
Language: English
Record Identifier: 99450795202621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Biotechnology & Applied Microbiology; Genetics & Heredity

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