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franciscozorrilla authored May 22, 2021
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![metawrapfigs_final4 001](https://user-images.githubusercontent.com/35606471/116543667-0d0f8f00-a8e6-11eb-835c-bc1fe935f43e.png)

`metaGEM` integrates an array of existing bioinformatics and metabolic modeling tools using Snakemake, for the purpose of predicting metabolic interactions within bacterial communities of microbiomes. From whole metagenome shotgun datasets, metagenome assembled genomes (MAGs) are reconstructed, which are then converted into genome-scale metabolic models (GEMs) for *in silico* simulations. Additional outputs include abundance estimates, taxonomic assignment, growth rate estimation, pangenome analysis, and eukaryotic MAG identification. The workflow diagram highlights the most important tasks in the core workflow on the left-hand column, whiel the auxiliary or supplementary tools are displayed on the right-hand column.
`metaGEM` is a Snakemake workflow that integrates an array of existing bioinformatics and metabolic modeling tools, for the purpose of predicting metabolic interactions within bacterial communities of microbiomes. From whole metagenome shotgun datasets, metagenome assembled genomes (MAGs) are reconstructed, which are then converted into genome-scale metabolic models (GEMs) for *in silico* simulations. Additional outputs include abundance estimates, taxonomic assignment, growth rate estimation, pangenome analysis, and eukaryotic MAG identification.

## 🌥️ Try it now

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git clone https://github.com/franciscozorrilla/metaGEM.git && cd metaGEM && rm -r .git && bash env_setup.sh
```

Congratulations, you can now start using `metaGEM`! Verify your installation by using the `check` task:
Congratulations, you can now start using `metaGEM`. Verify your installation by using the `check` task:

```
bash metaGEM.sh --task check
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## 💩 Tutorial

`metaGEM` can even be used to explore your own gut microbiome sequencing data from at-home-test-kit services such as [unseen bio](https://unseenbio.com/). The following tutorial showcases the `metaGEM` workflow on two unseenbio samples.
`metaGEM` can be used to explore your own gut microbiome sequencing data from at-home-test-kit services such as [unseen bio](https://unseenbio.com/). The following tutorial showcases the `metaGEM` workflow on two unseenbio samples.

[![Tutorial](https://img.shields.io/badge/metaGEM-Tutorial-%23d8b365)](https://github.com/franciscozorrilla/unseenbio_metaGEM)

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