Finding BGCs from antiSMASH database in metagenomes

This page summarizes the projects mentioned and recommended in the original post on /r/bioinformatics
metagenomics computational-biology metabolic-models gut-microbiome Snakemake

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  • metaGEM

    :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

    • One thing you could try is generating metagenome assembled genomes (MAGs) from each metagenome, use those MAGs to automatically reconstruct genome scale metabolic models (GEMs), and then do flux balance analysis (FBA) based simulations to compare the predicted metabolism across different treatments. We developed the metaGEM pipeline for exactly this purpose, you can read more about it here or check it out on GitHub

  • InfluxDB

    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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