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2018-05-18Zeitschriftenartikel DOI: 10.25646/5692
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
dc.contributor.authorWymant, Chris
dc.contributor.authorBlanquart, François
dc.contributor.authorGolubchik, Tanya
dc.contributor.authorGall, Astrid
dc.contributor.authorBakker, Margreet
dc.contributor.authorBezemer, Daniela
dc.contributor.authorCroucher, Nicholas J.
dc.contributor.authorHall, Matthew
dc.contributor.authorHillebregt, Mariska
dc.contributor.authorOng, Swee Hoe
dc.contributor.authorRatmann, Oliver
dc.contributor.authorAlbert, Jan
dc.contributor.authorBannert, Norbert
dc.contributor.authorFellay, Jacques
dc.contributor.authorFransen, Katrien
dc.contributor.authorGourlay, Annabelle
dc.contributor.authorGrabowski, M. Kate
dc.contributor.authorGunsenheimer-Bartmeyer, Barbara
dc.contributor.authorGünthard, Huldrych F.
dc.contributor.authorKivelä, Pia
dc.contributor.authorKouyos, Roger
dc.contributor.authorLaeyendecker, Oliver
dc.contributor.authorLiitsola, Kirsi
dc.contributor.authorMeyer, Laurence
dc.contributor.authorPorter, Kholoud
dc.contributor.authorRistola, Matti
dc.contributor.authorvan Sighem, Ard
dc.contributor.authorBerkhout, Ben
dc.contributor.authorCornelissen, Marion
dc.contributor.authorKellam, Paul
dc.contributor.authorReiss, Peter
dc.contributor.authorFraser, Christophe
dc.date.accessioned2018-09-18T12:55:31Z
dc.date.available2018-09-18T12:55:31Z
dc.date.issued2018-05-18none
dc.identifier.other10.1093/ve/vey007
dc.identifier.urihttp://edoc.rki.de/176904/5755
dc.description.abstractStudying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectbioinformaticseng
dc.subjectnext-generation sequencingeng
dc.subjectHIVeng
dc.subjectdiversityeng
dc.subjectgenome assemblyeng
dc.subjectmappingeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleEasy and accurate reconstruction of whole HIV genomes from short-read sequence data with shivernone
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:0257-176904/5755-9
dc.identifier.doihttp://dx.doi.org/10.25646/5692
dc.type.versionpublishedVersionnone
local.edoc.container-titleVirus Evolutionnone
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://academic.oup.com/ve/article/4/1/vey007/4999822none
local.edoc.container-publisher-nameOxford University Pressnone
local.edoc.container-volume4none
local.edoc.container-issue1none
local.edoc.container-reportyear2018none
local.edoc.container-firstpage1none
local.edoc.container-lastpage13none
local.edoc.rki-departmentInfektionsepidemiologienone
dc.description.versionPeer Reviewednone

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