metaGEM: create your own genome scale metabolic models directly from metagenomes

• ancient-microbiome-denovo

  1 4 0.0 Shell
  

In our pre-print, we apply metaGEM to samples from small lab cultures, human gut, plant-associated, bulk soil, and ocean metagenomes. Through pangenome analysis and species metabolic interaction analysis, we showed that the workflow generates phenotype-relevant and context-specific models. I have also applied metaGEM to kefir cultures and fossilized human poop with great success!

• 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

Although the workflow is meant to run on a high performance computer cluster (largely due to computational resources required for assembly), many steps can be run on a standard laptop. You can find code, documentation, and tutorials on GitHub! I am always looking for ways to improve the workflow's performance, accessibility, user experience, etc. so please let me know if you have any suggestions!

• InfluxDB

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  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• carveme

  2 138 5.0 Python

  CarveMe: genome-scale metabolic model reconstruction

Thanks sharing, I believe I have seen the github repo/paper before! Looks very interesting, I wonder if mantis could be used for expanding the functional annotation of sequences in the BiGG database (paper). This is the database that is used by CarveMe (paper) for building metabolic models from protein fasta files within the metaGEM workflow. I believe that CarveMe does not actually use the annotations themselves, but simply aligns sequences in a fasta file to the BiGG database, which contains associations between sequences -> genes -> reactions -> metabolites.

Suggest a related project