metaGEM

Reconstruction of genome scale metabolic models directly from metagenomes. A Snakemake-based workflow to generate high quality metagenome assembled genomes from short read paired-end data, reconstruct genome scale metabolic models, and perform community metabolic interaction simulations on high performance computing clusters. metaGEM integrates an array of existing bioinformatics and metabolic modeling tools using Snakemake, for the purpose of interrogating social interactions in bacterial communities of the human gut microbiome. From WMGS datasets, metagenome assembled genomes (MAGs) are reconstructed, which are then converted into genome-scale metabolic models (GEMs) for in silico simulations of cross feeding interactions within sample based communities. Additional outputs include abundance estimates, taxonomic assignment, growth rate estimation, pangenome analysis, and eukaryotic MAG identification.