Advice on how to go about genome scale metabolic model construction

• carveme

  2 138 5.0 Python

  CarveMe: genome-scale metabolic model reconstruction

Carveme: https://academic.oup.com/nar/article/46/15/7542/5042022 https://github.com/cdanielmachado/carveme https://carveme.readthedocs.io/en/latest/usage.html

• embl_gems

  2 24 10.0

  EMBL GEMs: A collection of GEnome-scale Models for bacterial species

Hi OP, what is your organism? Is it possible that a model already exists for that organism here (https://github.com/cdanielmachado/embl_gems)? If you are interested in reconstructing metabolic models directly from metagenomic samples then I can recommend the metaGEM pipeline, which uses CarveMe. In the paper we argue that metagenome-based metabolic models capture strain and context specific pangenomic variation that is missed by using reference genomes as a starting point of metabolic models 💎

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• metaGEM

  14 165 6.3 Python

  :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

GitHub: https://github.com/franciscozorrilla/metaGEM Paper: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab815/6382386

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