Skip to main content

A contig binning tool from viral metagenomes

Project description

Citation (Work in progress)

Arisdakessian C., Nigro O., Steward G., Poisson G., Belcaid M. CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning


CoCoNet (Composition and Coverage Network) is a binning method for viral metagenomes. It leverages deep learning to abstract the modeling of the k-mer composition and the coverage for binning contigs assembled form viral metagenomic data. Specifically, our method uses a neural network to learn from the metagenomic data a flexible function for predicting the probability that any pair of contigs originated from the same genome. These probabilities are subsequently combined to infer bins, or clusters representing the species present in the sequenced samples. Our approach was specifically designed for diverse viral metagenomes, such as those found in environmental samples (e.g., oceans, soil, etc.).


pip3 install --user numpy
pip3 install --user coconet-binning

For more installation options, see the documentation

Basic usage

CoCoNet is available as the command line program. For a list of all the options, open a terminal and run:

coconet run -h

For more details, please see the documentation on ReadTheDocs

Checking the installation

A test dataset is provided in this repository in tests/sim_data. To quickly verify the installation worked, you can simply download the repository and run the test command as follows:

git clone
cd CoCoNet
make test


Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

coconet-binning-1.1.0.tar.gz (37.6 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page