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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 14 hours ago
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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 (over 3 years ago)
Default Branch: main
Last Pushed: 2023-05-19T08:59:06.000Z (over 1 year ago)
Last Synced: 2024-12-15T12:44:38.386Z (7 days 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

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README

        ![logo](docs/imgs/meta_trans.png)

[![tests](https://github.com/Robaina/MetaTag/actions/workflows/tests.yml/badge.svg)](https://github.com/Robaina/MetaTag/actions/workflows/tests.yml)

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[![GitHub release](https://img.shields.io/github/release/Robaina/MetaTag.svg)](https://GitHub.com/Robaina/MetaTag/releases/)

![python](https://img.shields.io/badge/Python-3.10-blue)

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

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![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4)

[![DOI](https://zenodo.org/badge/379663963.svg)](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).