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BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 12, article id e0189256Article in journal (Refereed) Published
Abstract [en]

With the rapid advancement of high throughput sequencing, large numbers of genetic markers can be readily and cheaply acquired, but most current software packages for genetic map construction cannot handle such dense input. Modern computer architectures and server farms represent untapped resources that can be used to enable higher marker densities to be processed in tractable time. Here we present a pipeline using a modified version of OneMap that parallelizes over bottleneck functions and achieves substantial speedups for producing a high density linkage map (N = 20,000). Using simulated data we show that the outcome is as accurate as the traditional pipeline. We further demonstrate that there is a direct relationship between the number of markers used and the level of deviation between true and estimated order, which in turn impacts the final size of a genetic map.

Place, publisher, year, edition, pages
2017. Vol. 12, no 12, article id e0189256
National Category
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-144110DOI: 10.1371/journal.pone.0189256ISI: 000418564200037PubMedID: 29261725OAI: oai:DiVA.org:umu-144110DiVA, id: diva2:1176680
Available from: 2018-01-23 Created: 2018-01-23 Last updated: 2018-06-09Bibliographically approved

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Schiffthaler, BastianBernhardsson, CarolinaStreet, Nathaniel R.
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Umeå Plant Science Centre (UPSC)Department of Ecology and Environmental Sciences
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