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A Practical Guide to Phylogenetics for Nonexperts
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TreeToReads - a pipeline for simulating raw reads from phylogenies
Emily Jane McTavish1,2, James Pettengill3, Steven Davis3
1University of California, Merced, Merced, CA, USA. ejmctavish@ucmerced.edu.
BMC Bioinformatics
|March 22, 2017
Summary
TreeToReads simulates genomic data to test phylogenetic inference pipelines. This allows researchers to assess how parameter choices impact the accuracy of pathogen tracking and phylogenetic tree reconstruction.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Phylogenomic analysis is crucial for pathogen tracking in academia, public health, and industry.
- Multiple methods exist for inferring phylogenetic trees from genomic data, each with pros and cons.
- Existing methods lack comprehensive evaluation of parameter effects on phylogenetic tree accuracy.
Purpose of the Study:
- To introduce TreeToReads, a novel simulation pipeline.
- To enable controlled assessment of how various parameters influence phylogenetic tree reconstruction.
Main Methods:
- TreeToReads generates simulated raw read data from mutated genomes with a known phylogeny.
- The pipeline allows researchers to systematically vary parameters like sequence divergence and read coverage.
- This facilitates direct comparison of simulated and observed data to evaluate SNP calling and tree accuracy.
Main Results:
- The simulation approach allows for controlled testing of phylogenetic inference pipelines.
- Researchers can identify optimal parameter values for accurate SNP calling and tree reconstruction.
- This aids in understanding the robustness of different phylogenomic analysis tools.
Conclusions:
- Critical assessment of analytical pipeline accuracy and robustness is vital.
- TreeToReads provides a framework for rigorous evaluation of phylogenomic methods.
- This contributes to advancing both research and applied pathogen surveillance.
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