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TreeToReads - a pipeline for simulating raw reads from phylogenies

View ORCID ProfileEmily Jane McTavish, View ORCID ProfileJames Pettengill, View ORCID ProfileSteve Davis, View ORCID ProfileHugh Rand, View ORCID ProfileErrol Strain, View ORCID ProfileMarc Allard, View ORCID ProfileRuth E. Timme
doi: https://doi.org/10.1101/037655
Emily Jane McTavish
1Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence KS, USA
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James Pettengill
2Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD
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Steve Davis
2Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD
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Hugh Rand
2Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD
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Errol Strain
2Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD
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Marc Allard
2Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD
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Ruth E. Timme
2Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD
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Abstract

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 https://github.com/snacktavish/TreeToReads.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 22, 2016.
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TreeToReads - a pipeline for simulating raw reads from phylogenies
Emily Jane McTavish, James Pettengill, Steve Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E. Timme
bioRxiv 037655; doi: https://doi.org/10.1101/037655
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TreeToReads - a pipeline for simulating raw reads from phylogenies
Emily Jane McTavish, James Pettengill, Steve Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E. Timme
bioRxiv 037655; doi: https://doi.org/10.1101/037655

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