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BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species

Author

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  • Bastian Schiffthaler
  • Carolina Bernhardsson
  • Pär K Ingvarsson
  • Nathaniel R Street

Abstract

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.

Suggested Citation

  • Bastian Schiffthaler & Carolina Bernhardsson & Pär K Ingvarsson & Nathaniel R Street, 2017. "BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species," PLOS ONE, Public Library of Science, vol. 12(12), pages 1-12, December.
    • Handle: RePEc:plo:pone00:0189256
    DOI: 10.1371/journal.pone.0189256
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    References listed on IDEAS

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    1. Yonghui Wu & Prasanna R Bhat & Timothy J Close & Stefano Lonardi, 2008. "Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph," PLOS Genetics, Public Library of Science, vol. 4(10), pages 1-11, October.
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