Genin2 is a lightining-fast bioinformatic tool to predict genotypes for clade 2.3.4.4b H5Nx viruses collected in Europe since October 2020. Genotypes are assigned using the methods described in this article. Genin2 identifies only epidemiologically relevant European genotypes, i.e., detected in at least 3 viruses collected from at least 2 countries. You can inspect the up-to-date list of supported genotypes in this file.

Table of contents:

• Features
• Installation
• Usage
  • Input guidelines
  • Output format and interpretation
• FAQs
• How to cite Genin2
• License
• Fundings

Features

• Cross-platform: Genin2 can be run on any platform that supports the Python interpreter. Including, but not limited to: Windows, Linux, MacOS.
• Extremely lightweight: the prediction models weight less than 1 MB
• Easy on the resources: genin2 can be run on any laptop; 1 CPU and 200 MB of RAM is all it takes
• Lightning-fast: on a single 2.30 GHz core, Genin2 can process more than 1’200 sequences per minute

Cite Genin2

We are currently writing the paper. Until the publication please cite the GitHub repository:

https://github.com/izsvenezie-virology/genin2

License

Genin2 is licensed under the GNU Affero v3 license (see LICENSE).

Fundings

This work was supported by the NextGeneration EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project no. PE00000007, INF-ACT) and by Kappa-Flu project - Funded by the European Union under Grant Agreement (101084171). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or REA. Neither the European Union nor the granting authority can be held responsible for them.