RT Journal Article SR Electronic T1 Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.09.17.508371 DO 10.1101/2022.09.17.508371 A1 Matthew L Jenior A1 Emma M Glass A1 Jason A Papin YR 2022 UL http://biorxiv.org/content/early/2022/09/19/2022.09.17.508371.abstract AB Summary Genome-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 Implementation The 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.Contact Jason Papin: papin{at}virginia.eduCompeting Interest StatementThe authors have declared no competing interest.