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dc.contributor.author
Posada-Cespedes, Susana
dc.contributor.author
Seifert, David
dc.contributor.author
Beerenwinkel, Niko
dc.date.accessioned
2017-11-13T16:14:25Z
dc.date.available
2017-06-12T16:04:03Z
dc.date.available
2017-09-20T14:43:29Z
dc.date.available
2017-11-13T16:14:25Z
dc.date.issued
2017-07
dc.identifier.issn
0168-1702
dc.identifier.other
10.1016/j.virusres.2016.09.016
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/122719
dc.identifier.doi
10.3929/ethz-b-000122719
dc.description.abstract
Rapidly evolving RNA viruses prevail within a host as a collection of closely related variants, referred to as viral quasispecies. Advances in high-throughput sequencing (HTS) technologies have facilitated the assessment of the genetic diversity of such virus populations at an unprecedented level of detail. However, analysis of HTS data from virus populations is challenging due to short, error-prone reads. In order to account for uncertainties originating from these limitations, several computational and statistical methods have been developed for studying the genetic heterogeneity of virus population. Here, we review methods for the analysis of HTS reads, including approaches to local diversity estimation and global haplotype reconstruction. Challenges posed by aligning reads, as well as the impact of reference biases on diversity estimates are also discussed. In addition, we address some of the experimental approaches designed to improve the biological signal-to-noise ratio. In the future, computational methods for the analysis of heterogeneous virus populations are likely to continue being complemented by technological developments.
en_US
dc.format
application/pdf
dc.language.iso
en
en_US
dc.publisher
Elsevier
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject
Viral quasispecies
en_US
dc.subject
Genetic diversity
en_US
dc.subject
Haplotype reconstruction
en_US
dc.subject
Next-generation sequencing
en_US
dc.title
Recent advances in inferring viral diversity from high-throughput sequencing data
en_US
dc.type
Review Article
dc.rights.license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
dc.date.published
2016-09-28
ethz.journal.title
Virus research
ethz.journal.volume
239
en_US
ethz.journal.abbreviated
Virus Res
ethz.pages.start
17
en_US
ethz.pages.end
32
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.identifier.nebis
000025330
ethz.publication.place
Amsterdam
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::03790 - Beerenwinkel, Niko / Beerenwinkel, Niko
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::03790 - Beerenwinkel, Niko / Beerenwinkel, Niko
ethz.date.deposited
2017-06-12T16:06:23Z
ethz.source
ECIT
ethz.identifier.importid
imp593654dfeb75583332
ethz.ecitpid
pub:185046
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-09-20T14:43:33Z
ethz.rosetta.lastUpdated
2022-03-28T18:03:45Z
ethz.rosetta.versionExported
true
ethz.COinS
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