Published August 20, 2024 | Version 7.0.0
Software Open

Supporting data and code for "Data-driven recombination detection in viral genomes"

Creators

  • 1. Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy
  • 2. Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy

Description

Data and code for "Data-driven recombination detection in viral genomes". Alfonsi T., Bernasconi A., Chiara M., Ceri S.

The repository contains:

- A manuscript_supplementary_material, with a guide to the files

- The RecombinHunt application, with:

  • a README file including system requirements, installation guide (running recombinhunt-3.3.3-py3-none-any.whl), example code snippets;
  • a demo folder with Jupyter notebook (Python code) and example input/output datasets;
  • a src folder containing the source code;
  • a environments folder with preprocessed datasets and lineage/mutation probability tables
  • a validation_data folder with supporting files for 

Notes (English)

About version 7.0.0

This version of RecombinHunt is almost 90% faster than RecombinHunt v4 while maintaining the same accuracy and output. 

Information for the reviewers:
The repository version referenced in the manuscript Alfonsi, T., Bernasconi, A., Chiara, M. et al. Data-driven recombination detection in viral genomes. Nat Commun 15, 3313 (2024) is the Version 4 (recombinhunt-cov-3.3.3-v4.zip) released on March 13th, 2024

Information for the users:
If you are interested in using RecombinHunt for your own analyses, we suggest using this version to benefit from the following improvements:

  • ~88% faster analyses (measurements obtained by comparing the runtime for SARS-CoV-2 consesnus genomes on Nextstrain environment 2023-03-30)
  • the creation of environments without a specific set of variant candidates is now faster thanks to the new Environment's method copy_with_exclusions
  • better compatibility: RecombinHunt now supports the parquet file format for user-generated environments
  • the realtionship between candidates has been included in the Environment definition (see for example env_nextstrain_2023_03_30); RecombinHunt v7.0.0 is compatible the with environment files used with Recombinhunt v4

 

Notes (English)

This research was supported by the Ministero dell'Università e della Ricerca (MUR-ITA), within the PRIN PNRR 2022 SENSIBLE project (P2022CNN2J), funded by the European Union - Next Generation EU. 

Website: https://sensible-prin.github.io/

Files

recombinhunt-cov-7.0.0.zip

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