# 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.
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"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",
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