robaina / metatag

metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement

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💡 What is MetaTag?

This repository contains tools to assign taxonomy and function annotations to short reads through pylogenetic tree evolutionary placement.

🔧 Setup

The easiest way to use MetaTag is through the provided docker container. To use it, pull the image:

docker pull ghcr.io/robaina/metatag:latest

Then run the container interactively:

docker run -i ghcr.io/robaina/metatag:latest

Otherwise, you can install MetaTag like this:

1. Fork git repo into local machine (click on fork) and clone, or simply clone main branch with

git clone https://github.com/Robaina/MetaTag.git

2. CD to project MetaTag and set conda environment if not already set:

conda env create -n metatag -f envs/metatag-dev.yml

3. Build and install MetaTag:

conda activate metatag
(metatag) poetry build && pip install dist/metatag*.whl

Installation test

To check that everything is working properly, you can run a test what will perform the entire workflow on a minimal dataset. To run it, call bash script:

conda activate metatag
(metatag) bash tests/run_test.sh

or through Python's unittest module:

conda activate metatag
(metatag) python -m unittest tests/test_pipeline.py

It should produce a final tree with query sequences placed on it, as well as a bunch of intermediary files without any errors.

🚀 Usage

There are two main ways to use MetaTag: through the command line interface (CLI) or through the Python API. You can find an example of the API usage in the following Notebook:

• MetaTag API example

🔄 Dependencies

MetaTag would not work without these awesome projects:

• hmmer
• prodigal
• pyfastx
• biopython
• papara
• epa-ng
• gappa
• empress
• muscle
• mafft
• iqtree
• fasttree
• cd-hit
• repset
• seqkit
• numpy
• pandas
• psutil

Thanks!

Contributing

Contributions are always welcome! If you don't know where to start, you may find an interesting issue to work in here. Please, read our contribution guidelines first.

✒️ Citation

If you use MetaTag in your research, please cite it as follows:

Robaina Estévez, S., Fernández González, N., & González Hernández, J. M. (2023). metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement (Version v0.1.1) [Computer software]. https://doi.org/10.5281/zenodo.7949949

📄 License

This project is licensed under the terms of the Apache 2.0 license.