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What is metaGEM?

metaGEM is a Snakemake-based workflow designed 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. In the metaGEM manuscript we apply the workflow to lab culture, human gut, plant associated, bulk soil, and TARA oceans metagenomic samples.

Tutorial

A detailed tutorial of the metaGEM core workflow is demonstrated here.

Frequently asked questions

You can find answers to FAQs here.

Workflow

In the following pages of documentation we look "under the hood" of the Snakefile and discuss implementation details. For a more hands on demonstration of how to use metaGEM please see the tutorial above.

Core

0. metaGEM setup
1. Quality filter reads with fastp
2. Assembly with megahit
3. Draft bin sets with CONCOCT, MaxBin2, and MetaBAT2
4. Refine & reassemble bins with metaWRAP
5. Taxonomic assignment with GTDB-tk
6. Relative abundances with bwa
7. Reconstruct & evaluate genome-scale metabolic models with CarveMe and memote
8. Species metabolic coupling analysis with SMETANA

Bonus

9. Growth rate estimation
10. Pangenome analysis based on MAGs
11. Eukaryotic draft bins with EukRep and EukCC

Please cite

While the metaGEM publication is currently in the second round of revision please cite the pre-print if you use our pipeline in your research:

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes
Francisco Zorrilla, Kiran R. Patil, Aleksej Zelezniak
bioRxiv 2020.12.31.424982; doi: https://doi.org/10.1101/2020.12.31.424982