Restults generated for the metaGEM publication, where the following datasets were analyzed:
- 🧪 Small communities of gut microbes from lab cultures
- 💩 Real gut microbiome samples from Swedish diabetes paper
- 🪴 Plant-associated soil samples from Chinese rhizobiome study
- 🌏 Bulk-soil samples from Australian biodiversity analysis
- 🌊 Ocean water samples from global TARA Oceans expeditions
We provide an individual zenodo repo for each study, where you can find assemblies, contig coverage across all samples in dataset, metagenome assembled genomes (MAGs), ORF-annotated protein bins, and genome-scale metabolic models (GEMs). You can find statistics, summary files, and plots in the bonus.tar.gz folder, including taxonomic annotation of MAGs, as well as genome completeness & contamiantion estimates, among other intermediate results. Alternatively, if all you want is all of the metabolic models, they are collected in a single respository here:
| Dataset | Data Source | Number of Samples | Total Size (Gbp) | Number of MAGs Generated | metaGEM Results |
|---|---|---|---|---|---|
| Lab community | Publication | 48 | 37 | 154 | Zenodo |
| Human gut | Publication | 137 | 407 | 4134 | Zenodo |
| Plant associated | Publication | 6 | 40 | 172 | Zenodo |
| Bulk soil | Publication | 46 | 596 | 274 | Zenodo |
| TARA oceans | Publication | 246 | 4929 | 9366 | Zenodo (1/2), Zenodo (2/2) |
| TOTAL | - | 483 | 6009 | 14100 | - |
If you use metaGEM or results generated by the pipeline please consider citing the publication:
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes
Francisco Zorrilla, Filip Buric, Kiran R Patil, Aleksej Zelezniak
Nucleic Acids Research, 2021; gkab815, https://doi.org/10.1093/nar/gkab815
Please reach out with any comments, concerns, or discussions regarding metaGEM.
