https://github.com/robaina/metatag
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
https://github.com/robaina/metatag
bioinformatics evolutionary-placement function-annotation marine-microbiology metagenomics metagenomics-toolkit microbial-ecology taxonomy-assignment
Last synced: about 1 year ago
JSON representation
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
- Host: GitHub
- URL: https://github.com/robaina/metatag
- Owner: Robaina
- License: apache-2.0
- Created: 2021-06-23T16:21:10.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2023-05-19T08:59:06.000Z (about 3 years ago)
- Last Synced: 2025-04-06T10:38:01.271Z (about 1 year ago)
- Topics: bioinformatics, evolutionary-placement, function-annotation, marine-microbiology, metagenomics, metagenomics-toolkit, microbial-ecology, taxonomy-assignment
- Language: Python
- Homepage: https://robaina.github.io/MetaTag/
- Size: 70.3 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://github.com/Robaina/MetaTag/actions/workflows/tests.yml)
[](https://codecov.io/gh/Robaina/MetaTag)
[](https://GitHub.com/Robaina/MetaTag/releases/)
[](https://github.com/psf/black)
[](https://www.repostatus.org/#active)
[](https://zenodo.org/badge/latestdoi/379663963)
---
## :bulb: What is MetaTag?
This repository contains tools to assign taxonomy and function annotations to short reads through pylogenetic tree evolutionary placement.
## :wrench: Setup
The easiest way to use MetaTag is through the provided [docker](https://www.docker.com/) container. To use it, pull the image:
```bash
docker pull ghcr.io/robaina/metatag:latest
```
Then run the container interactively:
```bash
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
```bash
git clone https://github.com/Robaina/MetaTag.git
```
2. CD to project MetaTag and set conda environment if not already set:
```bash
conda env create -n metatag -f envs/metatag-dev.yml
```
3. Build and install MetaTag:
```bash
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:
```bash
conda activate metatag
(metatag) bash tests/run_test.sh
```
or through Python's unittest module:
```bash
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.
## :rocket: 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](docs/examples/example_api.ipynb)
## :arrows_counterclockwise: Dependencies
MetaTag would not work without these awesome projects:
- [hmmer](https://github.com/EddyRivasLab/hmmer)
- [prodigal](https://github.com/hyattpd/Prodigal)
- [pyfastx](https://github.com/lmdu/pyfastx)
- [biopython](https://github.com/biopython/biopython)
- [papara](https://cme.h-its.org/exelixis/web/software/papara/index.html)
- [epa-ng](https://github.com/Pbdas/epa-ng)
- [gappa](https://github.com/lczech/gappa)
- [empress](https://github.com/biocore/empress)
- [muscle](https://github.com/rcedgar/muscle)
- [mafft](https://github.com/GSLBiotech/mafft)
- [iqtree](https://github.com/Cibiv/IQ-TREE)
- [fasttree](https://github.com/PavelTorgashov/FastTree)
- [cd-hit](https://github.com/weizhongli/cdhit)
- [repset](https://onlinelibrary.wiley.com/doi/10.1002/prot.25461)
- [seqkit](https://github.com/shenwei356/seqkit)
- [numpy](https://github.com/numpy/numpy)
- [pandas](https://github.com/pandas-dev/pandas)
- [psutil](https://github.com/giampaolo/psutil)
Thanks!
## :octocat: Contributing
Contributions are always welcome! If you don't know where to start, you may find an interesting [issue to work in here](https://github.com/Robaina/MetaTag/issues). Please, read our [contribution guidelines](CONTRIBUTING.md) first.
## :black_nib: 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
## :page_facing_up: License
This project is licensed under the terms of the [Apache 2.0 license](LICENSE.md).