Presented at Evolution 2016

Research area: genomics

TreeToReads - a pipeline for simulating raw reads from phylogenies

Created on 22nd January 2016

Emily Jane McTavish; James Pettengill; Steven Davis; Hugh Rand; Errol Strain; Marc Allard; Ruth E Timme;

Using genome-wide SNP-based methods for tracking pathogens has become standard practice in academia and public health agencies. There are multiple computational approaches available that perform a similar task: call variants by mapping short read data against a reference genome, quality filter these variants, then concatenate the variants into a sequence matrix for downstream phylogenetic analysis. However, there are no existing methods to validate the accuracy of these approaches despite the fact that we know there are parameters that can affect whether a SNP is called, or the correct tree is recovered. We present a simulation approach (TreeToReads) to generate raw read data from mutated genomes simulated under a known phylogeny. The user can vary parameters of interest at each step in the simulation (e.g., topology, model of sequence evolution, and read coverage) to assess the robustness of a given result, which is critical within both research and applied settings. Source code, examples, and a tutorial are available at \url{}.

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