Recent advances in sequence assembly: Principles and applications

Chen, Q; Lan, C; Zhao, L; Wang, J; Chen, B; Chen, YPP

Recent advances in sequence assembly: Principles and applications

Chen, Q Lan, C Zhao, L Wang, J Chen, B Chen, YPP

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Publication Type:: Journal Article
Citation:: Briefings in Functional Genomics, 2017, 16 (6), pp. 361 - 378
Issue Date:: 2017-11-01

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Field	Value	Language
dc.contributor.author	Chen, Q	en_US
dc.contributor.author	Lan, C	en_US
dc.contributor.author	Zhao, L	en_US
dc.contributor.author	Wang, J	en_US
dc.contributor.author	Chen, B	en_US
dc.contributor.author	Chen, YPP	en_US
dc.date.issued	2017-11-01	en_US
dc.identifier.citation	Briefings in Functional Genomics, 2017, 16 (6), pp. 361 - 378	en_US
dc.identifier.issn	2041-2649	en_US
dc.identifier.uri	http://hdl.handle.net/10453/127376
dc.description.abstract	© The Author 2017. Published by Oxford University Press. All rights reserved. The application of advanced sequencing technologies and the rapid growth of various sequence data have led to increasing interest in DNA sequence assembly. However, repeats and polymorphismoccur frequently in genomes, and each of these has different impacts on assembly. Further, many new applications for sequencing, such as metagenomics regarding multiple species, have emerged in recent years. These not only give rise to higher complexity but also prevent short-read assembly in an efficient way. This article reviews the theoretical foundations that underlie current mapping-based assembly and de novo-based assembly, and highlights the key issues and feasible solutions that need to be considered. It focuses on how individual processes, such as optimal k-mer determination and error correction in assembly, rely on intelligent strategies or high-performance computation. We also survey primary algorithms/software and offer a discussion on the emerging challenges in assembly.	en_US
dc.relation.ispartof	Briefings in Functional Genomics	en_US
dc.relation.isbasedon	10.1093/bfgp/elx006	en_US
dc.subject.mesh	DNA	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Polymorphism, Single Nucleotide	en_US
dc.subject.mesh	Algorithms	en_US
dc.subject.mesh	Computer Graphics	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Metagenomics	en_US
dc.title	Recent advances in sequence assembly: Principles and applications	en_US
dc.type	Journal Article
utslib.citation.volume	6	en_US
utslib.citation.volume	16	en_US
utslib.for	0803 Computer Software	en_US
utslib.for	0604 Genetics	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Students
utslib.copyright.status	closed_access
pubs.issue	6	en_US
pubs.publication-status	Published	en_US
pubs.volume	16	en_US

Abstract:

© The Author 2017. Published by Oxford University Press. All rights reserved. The application of advanced sequencing technologies and the rapid growth of various sequence data have led to increasing interest in DNA sequence assembly. However, repeats and polymorphismoccur frequently in genomes, and each of these has different impacts on assembly. Further, many new applications for sequencing, such as metagenomics regarding multiple species, have emerged in recent years. These not only give rise to higher complexity but also prevent short-read assembly in an efficient way. This article reviews the theoretical foundations that underlie current mapping-based assembly and de novo-based assembly, and highlights the key issues and feasible solutions that need to be considered. It focuses on how individual processes, such as optimal k-mer determination and error correction in assembly, rely on intelligent strategies or high-performance computation. We also survey primary algorithms/software and offer a discussion on the emerging challenges in assembly.

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http://hdl.handle.net/10453/127376