Show simple item record

dc.contributor.authorSchroder, J
dc.contributor.authorWirawan, A
dc.contributor.authorSchmidt, B
dc.contributor.authorPapenfuss, AT
dc.date.accessioned2020-12-21T01:35:17Z
dc.date.available2020-12-21T01:35:17Z
dc.date.issued2017-07-20
dc.identifierpii: 10.1186/s12859-017-1760-3
dc.identifier.citationSchroder, J., Wirawan, A., Schmidt, B. & Papenfuss, A. T. (2017). CLOVE: classification of genomic fusions into structural variation events. BMC BIOINFORMATICS, 18 (1), https://doi.org/10.1186/s12859-017-1760-3.
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11343/256572
dc.description.abstractBACKGROUND: A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than one breakpoint or fusion). RESULTS: We present CLOVE, an algorithm for integrating the results of multiple breakpoint or SV callers and classifying the results as a particular SV. CLOVE is based on a graph data structure that is created from the breakpoint information. The algorithm looks for patterns in the graph that are characteristic of more complex rearrangement types. CLOVE is able to integrate the results of multiple callers, producing a consensus call. CONCLUSIONS: We demonstrate using simulated and real data that re-classified SV calls produced by CLOVE improve on the raw call set of existing SV algorithms, particularly in terms of accuracy. CLOVE is freely available from http://www.github.com/PapenfussLab .
dc.languageEnglish
dc.publisherBIOMED CENTRAL LTD
dc.titleCLOVE: classification of genomic fusions into structural variation events
dc.typeJournal Article
dc.identifier.doi10.1186/s12859-017-1760-3
melbourne.affiliation.departmentMedical Biology (W.E.H.I.)
melbourne.affiliation.departmentComputing and Information Systems
melbourne.source.titleBMC Bioinformatics
melbourne.source.volume18
melbourne.source.issue1
dc.rights.licenseCC BY
melbourne.elementsid1224235
melbourne.contributor.authorSchroeder, Jan
melbourne.contributor.authorPapenfuss, Anthony
dc.identifier.eissn1471-2105
melbourne.accessrightsOpen Access


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record