{"id":16265063,"url":"https://github.com/robaina/metatag","last_synced_at":"2025-04-08T14:29:48.236Z","repository":{"id":123132128,"uuid":"379663963","full_name":"Robaina/MetaTag","owner":"Robaina","description":"metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement","archived":false,"fork":false,"pushed_at":"2023-05-19T08:59:06.000Z","size":73759,"stargazers_count":1,"open_issues_count":2,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-06T10:38:01.271Z","etag":null,"topics":["bioinformatics","evolutionary-placement","function-annotation","marine-microbiology","metagenomics","metagenomics-toolkit","microbial-ecology","taxonomy-assignment"],"latest_commit_sha":null,"homepage":"https://robaina.github.io/MetaTag/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Robaina.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-06-23T16:21:10.000Z","updated_at":"2023-05-25T12:24:58.000Z","dependencies_parsed_at":null,"dependency_job_id":"46ce7a08-da4e-46dc-8aac-4fd5cec32c54","html_url":"https://github.com/Robaina/MetaTag","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FMetaTag","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FMetaTag/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FMetaTag/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FMetaTag/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Robaina","download_url":"https://codeload.github.com/Robaina/MetaTag/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247860197,"owners_count":21008250,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","evolutionary-placement","function-annotation","marine-microbiology","metagenomics","metagenomics-toolkit","microbial-ecology","taxonomy-assignment"],"created_at":"2024-10-10T17:05:57.063Z","updated_at":"2025-04-08T14:29:48.204Z","avatar_url":"https://github.com/Robaina.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![logo](docs/imgs/meta_trans.png)\n\n[![tests](https://github.com/Robaina/MetaTag/actions/workflows/tests.yml/badge.svg)](https://github.com/Robaina/MetaTag/actions/workflows/tests.yml)\n[![codecov](https://codecov.io/gh/Robaina/MetaTag/branch/main/graph/badge.svg?token=PY48LGP84S)](https://codecov.io/gh/Robaina/MetaTag)\n[![GitHub release](https://img.shields.io/github/release/Robaina/MetaTag.svg)](https://GitHub.com/Robaina/MetaTag/releases/)\n\n![python](https://img.shields.io/badge/Python-3.10-blue)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n\n![license](https://img.shields.io/github/license/Robaina/MetaTag)\n![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4)\n\n[![DOI](https://zenodo.org/badge/379663963.svg)](https://zenodo.org/badge/latestdoi/379663963)\n\n---\n## :bulb: What is MetaTag?\nThis repository contains tools to assign taxonomy and function annotations to short reads through pylogenetic tree evolutionary placement.\n\n## :wrench: Setup\nThe easiest way to use MetaTag is through the provided [docker](https://www.docker.com/) container. To use it, pull the image:\n\n```bash\ndocker pull ghcr.io/robaina/metatag:latest\n```\n\nThen run the container interactively:\n\n```bash\ndocker run -i ghcr.io/robaina/metatag:latest\n```\n\nOtherwise, you can install MetaTag like this:\n\n1. Fork git repo into local machine (click on fork) and clone, or simply clone main branch with\n```bash\ngit clone https://github.com/Robaina/MetaTag.git\n```\n\n2. CD to project MetaTag and set conda environment if not already set:\n```bash\nconda env create -n metatag -f envs/metatag-dev.yml\n```\n\n3. Build and install MetaTag:\n```bash\nconda activate metatag\n(metatag) poetry build \u0026\u0026 pip install dist/metatag*.whl\n```\n### Installation test\nTo 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:\n```bash\nconda activate metatag\n(metatag) bash tests/run_test.sh\n```\n\nor through Python's unittest module:\n```bash\nconda activate metatag\n(metatag) python -m unittest tests/test_pipeline.py\n```\n\nIt should produce a final tree with query sequences placed on it, as well as a bunch of intermediary files without any errors.\n\n## :rocket: Usage\nThere 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:\n\n* [MetaTag API example](docs/examples/example_api.ipynb)\n\n## :arrows_counterclockwise: Dependencies\nMetaTag would not work without these awesome projects:\n\n- [hmmer](https://github.com/EddyRivasLab/hmmer)\n- [prodigal](https://github.com/hyattpd/Prodigal)\n- [pyfastx](https://github.com/lmdu/pyfastx)\n- [biopython](https://github.com/biopython/biopython)\n- [papara](https://cme.h-its.org/exelixis/web/software/papara/index.html)\n- [epa-ng](https://github.com/Pbdas/epa-ng)\n- [gappa](https://github.com/lczech/gappa)\n- [empress](https://github.com/biocore/empress)\n- [muscle](https://github.com/rcedgar/muscle)\n- [mafft](https://github.com/GSLBiotech/mafft)\n- [iqtree](https://github.com/Cibiv/IQ-TREE)\n- [fasttree](https://github.com/PavelTorgashov/FastTree)\n- [cd-hit](https://github.com/weizhongli/cdhit)\n- [repset](https://onlinelibrary.wiley.com/doi/10.1002/prot.25461)\n- [seqkit](https://github.com/shenwei356/seqkit)\n- [numpy](https://github.com/numpy/numpy)\n- [pandas](https://github.com/pandas-dev/pandas)\n- [psutil](https://github.com/giampaolo/psutil)\n\nThanks!\n\n## :octocat: Contributing\n\nContributions 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.\n\n## :black_nib: Citation\n\nIf you use MetaTag in your research, please cite it as follows:\n\n\u003e Robaina Estévez, S., Fernández González, N., \u0026 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\n\n## :page_facing_up: License\n\nThis project is licensed under the terms of the [Apache 2.0 license](LICENSE.md).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobaina%2Fmetatag","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frobaina%2Fmetatag","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobaina%2Fmetatag/lists"}