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dc.contributor.authorIllingworth, Christopheren
dc.date.accessioned2016-04-29T09:22:30Z
dc.date.available2016-04-29T09:22:30Z
dc.date.issued2016-04-22en
dc.identifier.citationC. J. R. Illingworth. Bioinformatics (2016). DOI:10.1093/bioinformatics/btw205en
dc.identifier.issn1367-4803
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/255804
dc.description.abstractAn increasingly common method for studying evolution is the collection of time-resolved short-read sequence data. Such datasets allow for the direct observation of rapid evolutionary processes, as might occur in natural microbial populations and in evolutionary experiments. In many circumstances, evolutionary pressure acting upon single variants can cause genomic changes at multiple nearby loci. SAMFIRE is an open-access software package for processing and analysing sequence reads from time-resolved data, calling important single- and multi-locus variants over time, identifying alleles potentially affected by selection, calculating linkage disequilibrium statistics, performing haplotype reconstruction, and exploiting time-resolved information to estimate the extent of uncertainty in reported genomic data.
dc.description.sponsorshipCI was supported by a Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and the Royal Society (Grant Number 101239/Z/13/Z).
dc.languageEnglishen
dc.language.isoenen
dc.publisherOxford University Press
dc.titleSAMFIRE: multi-locus variant calling for time-resolved sequence dataen
dc.typeArticle
dc.provenanceOA-8202
dc.description.versionThis is the author accepted manuscript. The final version is available from Oxford University Press via http://dx.doi.org/10.1093/bioinformatics/btw205en
prism.publicationDate2016en
prism.publicationNameBioinformaticsen
dc.rioxxterms.funderWellcome Trust
dcterms.dateAccepted2016-04-10en
rioxxterms.versionofrecord10.1093/bioinformatics/btw205en
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2016-04-22en
dc.contributor.orcidIllingworth, Christopher [0000-0002-0030-2784]
dc.identifier.eissn1367-4811
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idWellcome Trust (101239/Z/13/Z)
rioxxterms.freetoread.startdate2017-04-22


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