ISMB 2015 Poster submission
Towards an interoperating ecosystem of tools and resources for population genetics in R
The broad and inexpensive availability of modern next-generation sequencing and genotyping technologies have led to a wealth of data and analytical methods for population genetics research. In the popular statistical and mathematical computing platform R alone, there are now dozens of packages available for analyzing and visualizing population genetics data. However, this organically grown wealth of methods and packages, combined with the exponential growth of datasets, has also created challenges for researchers to take full advantage of these resources. It can be difficult to know which R packages are best used, and many packages do not interoperate well. A common base class that provides efficient storage of genetic data and promotes interoperability remains lacking even though the need was identified years ago. Current implementations often do not scale well to the kind of large volume datasets that are increasingly common. Creating complex analysis workflows that need to pass data, metadata, and other state information from one package to another can be challenging. To address these gaps, we held the Population Genetics in R Hackathon at, and sponsored by the National Evolutionary Synthesis Center (NESCent), located in Durham, NC. We designed the event to target interoperability, scalability, and workflow building challenges among the many population genetics R packages that already exist, and to ultimately help foster an interoperating ecosystem of tools and resources for both users and researcher-developers. Here we highlight key outcomes of the event, which are all open-source and freely available. For details see https://github.com/NESCent/r-popgen-hackathon/.