metaGEM: metagenomes -> genomes -> metabolic models

• 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

Hi all, I made a post a while back advertising the metaGEM pipeline for reconstructing metagenome assembled genomes (MAGs) and genome scale metabolic models (GEMs) from metagenomes. The paper has now been published in Nucleic Acids Research, I hope some of you here may find it interesting or useful for your own research! I will also leave the GitHub repo here 💻 🧬

• embl_gems

  2 24 10.0

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

Regarding your question about a reference database, we have deposited the models in a zenodo repository for now (https://zenodo.org/record/4407746#.YWFXFBbRYWM), but I do plan on making them more accessible (e.g. https://github.com/cdanielmachado/embl_gems) and also providing the underlying genomes + taxonomic annotation and other info/metadata generated by metaGEM.

• InfluxDB

  www.influxdata.com sponsored

  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.

  

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