PRECOG: PREsentation and Characterization Of Growth-data
Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental configuration at a massive scale. For microbes, the key organismal phenotype is the growth in population size because it contains information that is directly linked to fitness. Our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology.
To automate visualization, analysis and exploration of complex and high-resolution microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics.
Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to other complex procedures like fitting. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits indicating the need for proper standardization in data analysis.
PRECOG is a tool computational framework that will streamline phenotypic trait extraction, its storage, visualization, distribution and the creation of vast and informative phenomics databases.