BatchMap: A Parallel Implementation of the OneMap R Package for Fast Computation of F1 Linkage Maps in Outcrossing Species

PLoS One. 2017 Dec 20;12(12):e0189256. doi: 10.1371/journal.pone.0189256. eCollection 2017.

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.

MeSH terms

  • Genetic Linkage*
  • High-Throughput Nucleotide Sequencing
  • Software*

Grant support

This study was supported by funding from the Knut and Alice Wallenberg foundation. NRS is supported by the Trees and Crops for the Future (TC4F) program. This work was supported by funds from the Swedish Research Council (VR), the Swedish Governmental Agency for Innovation Systems (VINNOVA), The Swedish Research Council (FORMAS) through the UPSC Berzelii Centre for Forest Biotechnology.