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bioRxiv · 10.1101/2022.09.17.508371

Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling

Jenior, M. L.·Glass, E. M.·Papin, J. A.
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Abstract

SummaryGenome-scale metabolic network reconstructions (GENREs) are valuable for understanding cellular metabolism in silico. Several tools exist for automatic GENRE generation. However, these tools frequently (1) do not readily integrate with some of the widely-used suites of packaged methods available for network analysis, (2) lack effective network curation tools, and (3) are not sufficiently user-friendly. Here, we present Reconstructor, a user-friendly COBRApy compatible tool with ModelSEED namespace compatibility and a pFBA-based gap-filling technique. We demonstrate how Reconstructor readily generates high-quality GENRES that are useful for further biological discovery. Availability and ImplementationThe Reconstructor package is freely available for download via pip in the command line (pip install reconstructor). Usage instructions and benchmarking data are available at http://github.com/emmamglass/reconstructor. ContactJason Papin: papin@virginia.edu

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Jenior, M. L., Glass, E. M., Papin, J. A.. 2022-09-19. Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling. https://doi.org/10.1101/2022.09.17.508371

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