DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

MOTIVATION: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account. RESULTS: We developed Data-drivEn METabolic nEtwork Refinement (DEMETER), a Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension, which enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data and refinement of pathways based on manually refined genome annotations. AVAILABILITY AND IMPLEMENTATION: DEMETER and tutorials are freely available at https://github.com/opencobra. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.