A Systematic Assessment of Current Genome-Scale Metabolic Reconstruction Tools

Several genome-scale metabolic reconstruction software platforms have been developed and continuously updated during the last fifteen years. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. So far, these platforms have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality genome-scale metabolic models. In consequence, this lack of assessment keeps users away from selecting the tool that best fits the purpose of their research. In this work, we reviewed the current genome-scale reconstruction software platforms and we performed a systematic assessment of the most promising tools. We defined a list of features for assessing software quality related to genome-scale reconstruction which we hope it would be useful for potential users. In addition, we compared the output networks generated using each of these tools with the high-quality manually curated models of Lactobacillus plantarum and Bortedella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We showed that none of the tools outperform the others in all the studied features and that users should carefully choose one or another, or even combining them, depending on the particularities of their projects.