metatag
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
Science Score: 67.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: wiley.com, zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (19.5%) to scientific vocabulary
Keywords
Repository
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
Basic Info
- Host: GitHub
- Owner: Robaina
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://robaina.github.io/MetaTag/
- Size: 70.3 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 2
- Releases: 3
Topics
Metadata Files
README.md
: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 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:
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.gitCD to project MetaTag and set conda environment if not already set:
bash conda env create -n metatag -f envs/metatag-dev.ymlBuild and install MetaTag:
bash conda activate metatag (metatag) poetry build && pip install dist/metatag*.whlInstallation 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:
:arrows_counterclockwise: 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!
:octocat: 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.
: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
:pagefacingup: License
This project is licensed under the terms of the Apache 2.0 license.
Owner
- Name: Semidán Robaina
- Login: Robaina
- Kind: user
- Location: Atlantic Ocean
- Company: Hapdera
- Website: https://www.linkedin.com/in/semidan-robaina/
- Twitter: srobainae
- Repositories: 12
- Profile: https://github.com/Robaina
Computational Biology | Data Science | Python Dev. | Ph.D. Systems Biology
Citation (CITATION.cff)
# YAML 1.2
---
abstract: "metaTAG: functional and taxonomical annotation of metagenomes through phylogenetic tree placement"
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
-
family-names: "Robaina Estévez"
given-names: "Semidán"
orcid: "https://orcid.org/0000-0003-0781-1677"
affiliation: "Department of Microbiology. University of La Laguna. Spain"
email: "srobaina@ull.edu.es"
-
family-names: "Fernández González"
given-names: "Nuria"
orcid: "https://orcid.org/0000-0002-7468-9643"
affiliation: "Microbiome Analysis Laboratory. CNB-CSIC. Spain."
email: "nfernandez@cnb.csic.es"
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family-names: "González Hernández"
given-names: "José Manuel"
orcid: "https://orcid.org/0000-0002-9926-3323"
affiliation: "Department of Microbiology. University of La Laguna. Spain"
email: "jmglezh@ull.edu.es"
title: "metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement"
version: v0.1.1
doi: 10.5281/zenodo.7949949
date-released: 2023-05-19
url: "https://github.com/Robaina/MetaTag"
---
GitHub Events
Total
Last Year
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Semidán Robaina Estévez | s****a@g****m | 602 |
| jmglezh | 4****h | 18 |
| Semidán Robaina Estévez | h****o@s****m | 17 |
| micronuria | 9****a | 2 |
| gonzalez | g****z@p****s | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 115
- Total pull requests: 60
- Average time to close issues: about 1 month
- Average time to close pull requests: about 8 hours
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 1.49
- Average comments per pull request: 0.22
- Merged pull requests: 55
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Robaina (49)
- micronuria (13)
- gecko1990 (5)
Pull Request Authors
- Robaina (33)