PDR: a new genome assembly evaluation metric based on genetics concerns.

Xie, L; Wong, L

PDR: a new genome assembly evaluation metric based on genetics concerns.

Xie, L Wong, L

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Publisher:: Oxford University Press (OUP)
Publication Type:: Journal Article
Citation:: Bioinformatics, 2021, 37, (3), pp. 289-295
Issue Date:: 2021-04-20

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Field	Value	Language
dc.contributor.author	Xie, L
dc.contributor.author	Wong, L
dc.date.accessioned	2022-08-06T05:46:00Z
dc.date.available	2020-07-30
dc.date.available	2022-08-06T05:46:00Z
dc.date.issued	2021-04-20
dc.identifier.citation	Bioinformatics, 2021, 37, (3), pp. 289-295
dc.identifier.issn	1367-4803
dc.identifier.issn	1367-4811
dc.identifier.uri	http://hdl.handle.net/10453/159698
dc.description.abstract	MOTIVATION: Existing genome assembly evaluation metrics provide only limited insight on specific aspects of genome assembly quality, and sometimes even disagree with each other. For better integrative comparison between assemblies, we propose, here, a new genome assembly evaluation metric, Pairwise Distance Reconstruction (PDR). It derives from a common concern in genetic studies, and takes completeness, contiguity, and correctness into consideration. We also propose an approximation implementation to accelerate PDR computation. RESULTS: Our results on publicly available datasets affirm PDR's ability to integratively assess the quality of a genome assembly. In fact, this is guaranteed by its definition. The results also indicated the error introduced by approximation is extremely small and thus negligible. AVAILABILITYAND IMPLEMENTATION: https://github.com/XLuyu/PDR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
dc.format	Print
dc.language	eng
dc.publisher	Oxford University Press (OUP)
dc.relation.ispartof	Bioinformatics
dc.relation.isbasedon	10.1093/bioinformatics/btaa704
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	01 Mathematical Sciences, 06 Biological Sciences, 08 Information and Computing Sciences
dc.subject.classification	Bioinformatics
dc.subject.mesh	Genome
dc.subject.mesh	High-Throughput Nucleotide Sequencing
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Software
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Genome
dc.subject.mesh	Software
dc.subject.mesh	High-Throughput Nucleotide Sequencing
dc.title	PDR: a new genome assembly evaluation metric based on genetics concerns.
dc.type	Journal Article
utslib.citation.volume	37
utslib.location.activity	England
utslib.for	01 Mathematical Sciences
utslib.for	06 Biological Sciences
utslib.for	08 Information and Computing Sciences
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
utslib.copyright.status	closed_access	*
dc.date.updated	2022-08-06T05:45:59Z
pubs.issue	3
pubs.publication-status	Published
pubs.volume	37
utslib.citation.issue	3

Abstract:

MOTIVATION: Existing genome assembly evaluation metrics provide only limited insight on specific aspects of genome assembly quality, and sometimes even disagree with each other. For better integrative comparison between assemblies, we propose, here, a new genome assembly evaluation metric, Pairwise Distance Reconstruction (PDR). It derives from a common concern in genetic studies, and takes completeness, contiguity, and correctness into consideration. We also propose an approximation implementation to accelerate PDR computation. RESULTS: Our results on publicly available datasets affirm PDR's ability to integratively assess the quality of a genome assembly. In fact, this is guaranteed by its definition. The results also indicated the error introduced by approximation is extremely small and thus negligible. AVAILABILITYAND IMPLEMENTATION: https://github.com/XLuyu/PDR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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http://hdl.handle.net/10453/159698