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.
CoCoPyE is available via pip and conda (conda-forge channel). See the project wiki for installation and usage instructions.
You can test CoCoPyE without installation on our project homepage. 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.
For bug reports, suggestions or questions, please open an issue on GitHub or send an email to [email protected].
You can find the API documentation of the CoCoPyE package on https://gobics.github.io/cocopye.
CoCoPyE is available under the terms of the GNU General Public License, version 3 or later. See COPYING for the full license text.