Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We developed DEMETER, a COBRA Toolbox extension that 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: DEMETER and tutorials are available at https://github.com/opencobra/cobratoolbox.
@article{arxiv.2106.06638,
title = {DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations},
author = {Almut Heinken and Stefanía Magnúsdóttir and Ronan M. T. Fleming and Ines Thiele},
journal= {arXiv preprint arXiv:2106.06638},
year = {2021}
}