# CoCoPyE
**CoCoPyE is a fast tool for quality assessment of microbial genomes. It is able to reliably predict
completeness and contamination of bacterial and archaeal genomes. Additionally, it can provide a
taxonomic classification of the input.**
Background: The classical approach for estimation of quality indices solely relies on a relatively small
number of universal single copy genes. Because these classical markers only cover a small fraction of the
whole genome the quality assessment can be rather unreliable. Our method is based on a novel
two-stage feature extraction and transformation scheme. It first performs a flexible extraction
of genomic markers and then refines the marker-based estimates with a machine learning approach based on
count-ratio histograms. In our simulation studies CoCoPyE showed a more accurate prediction of quality
indices than existing tools.
## Getting started
CoCoPyE is available via pip and conda (conda-forge channel). See the [project wiki](https://github.com/gobics/cocopye/wiki)
for installation and usage instructions.
- [Quickstart](https://github.com/gobics/cocopye/wiki/Quickstart)
- [Installation](https://github.com/gobics/cocopye/wiki/Installation)
- [Usage](https://github.com/gobics/cocopye/wiki/Usage)
### Online Demo
You can test CoCoPyE without installation on [our project homepage](https://cocopye.uni-goettingen.de). Please note that the online demo can process only
one query genome per request and is less performant than a local installation. Therefore it is highly recommended to use the online
version only for evaluation purposes and install CoCoPyE on your own machine for productive use.
## Additional notes
### Contact
For bug reports, suggestions or questions, please open an issue on [GitHub](https://github.com/gobics/cocopye/issues)
or send an email to [pmeinic@gwdg.de](mailto:pmeinic@gwdg.de).
### API documentation
You can find the API documentation of the CoCoPyE package on [https://gobics.github.io/cocopye](https://gobics.github.io/cocopye).
### License
CoCoPyE is available under the terms of the GNU General Public License, version 3 or later. See [`COPYING`](https://github.com/gobics/cocopye/blob/master/COPYING) for the full license text.
Raw data
{
"_id": null,
"home_page": null,
"name": "cocopye",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": "Niklas Birth <birth@posteo.de>",
"keywords": "bioinformatics, biology, microbiology, metagenomics, genome, genome quality",
"author": "Niklas Birth, Nicolina Leppich, Dr. Peter Meinicke",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/a8/88/0020528d3957271b9a5c1f4434558553720afa1eb1586b4727dd42955f57/cocopye-0.5.0.tar.gz",
"platform": null,
"description": "# CoCoPyE\n\n**CoCoPyE is a fast tool for quality assessment of microbial genomes. It is able to reliably predict\ncompleteness and contamination of bacterial and archaeal genomes. Additionally, it can provide a\ntaxonomic classification of the input.**\n\nBackground: The classical approach for estimation of quality indices solely relies on a relatively small\nnumber of universal single copy genes. Because these classical markers only cover a small fraction of the\nwhole genome the quality assessment can be rather unreliable. Our method is based on a novel\ntwo-stage feature extraction and transformation scheme. It first performs a flexible extraction\nof genomic markers and then refines the marker-based estimates with a machine learning approach based on\ncount-ratio histograms. In our simulation studies CoCoPyE showed a more accurate prediction of quality\nindices than existing tools.\n\n## Getting started\n\nCoCoPyE is available via pip and conda (conda-forge channel). See the [project wiki](https://github.com/gobics/cocopye/wiki)\nfor installation and usage instructions.\n\n- [Quickstart](https://github.com/gobics/cocopye/wiki/Quickstart)\n- [Installation](https://github.com/gobics/cocopye/wiki/Installation)\n- [Usage](https://github.com/gobics/cocopye/wiki/Usage)\n\n### Online Demo\n\nYou can test CoCoPyE without installation on [our project homepage](https://cocopye.uni-goettingen.de). Please note that the online demo can process only \none query genome per request and is less performant than a local installation. Therefore it is highly recommended to use the online\nversion only for evaluation purposes and install CoCoPyE on your own machine for productive use.\n\n## Additional notes\n\n### Contact\n\nFor bug reports, suggestions or questions, please open an issue on [GitHub](https://github.com/gobics/cocopye/issues)\nor send an email to [pmeinic@gwdg.de](mailto:pmeinic@gwdg.de).\n\n### API documentation\n\nYou can find the API documentation of the CoCoPyE package on [https://gobics.github.io/cocopye](https://gobics.github.io/cocopye).\n\n### License\n\nCoCoPyE is available under the terms of the GNU General Public License, version 3 or later. See [`COPYING`](https://github.com/gobics/cocopye/blob/master/COPYING) for the full license text.\n",
"bugtrack_url": null,
"license": "GPL-3.0-or-later",
"summary": "Feature-based prediction of genome quality indices",
"version": "0.5.0",
"project_urls": {
"Documentation": "https://github.com/gobics/cocopye/wiki",
"Homepage": "https://cocopye.uni-goettingen.de",
"Source": "https://github.com/gobics/cocopye"
},
"split_keywords": [
"bioinformatics",
" biology",
" microbiology",
" metagenomics",
" genome",
" genome quality"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "a404a8857b3aec96005a2c5db5b5fa84939af3dc14d605db168a3e2700ed21c8",
"md5": "bfa9555fea040c3f8b748b927472c5bf",
"sha256": "6219ae7d49d4a8fd49075931b75f5340f4c384955830c2f0ab1a0cc15adf26fb"
},
"downloads": -1,
"filename": "cocopye-0.5.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "bfa9555fea040c3f8b748b927472c5bf",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 16130588,
"upload_time": "2024-07-17T22:59:21",
"upload_time_iso_8601": "2024-07-17T22:59:21.059114Z",
"url": "https://files.pythonhosted.org/packages/a4/04/a8857b3aec96005a2c5db5b5fa84939af3dc14d605db168a3e2700ed21c8/cocopye-0.5.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "a8880020528d3957271b9a5c1f4434558553720afa1eb1586b4727dd42955f57",
"md5": "f8864c06b7b0cba9d09db807682bac16",
"sha256": "aef29373a987bb5492f1ffba83cf22e25c4008a0ded57864f00ced45b23af67a"
},
"downloads": -1,
"filename": "cocopye-0.5.0.tar.gz",
"has_sig": false,
"md5_digest": "f8864c06b7b0cba9d09db807682bac16",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 16101927,
"upload_time": "2024-07-17T22:59:24",
"upload_time_iso_8601": "2024-07-17T22:59:24.372684Z",
"url": "https://files.pythonhosted.org/packages/a8/88/0020528d3957271b9a5c1f4434558553720afa1eb1586b4727dd42955f57/cocopye-0.5.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-07-17 22:59:24",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "gobics",
"github_project": "cocopye",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "cocopye"
}
JSON
