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Pui, C.S.; Fumagalli, M.; Mathieson, S.

Python code for building and training a generative adversarial network for demographic inferences from genomic data

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https://doi.org/10.5285/3ae572f6-4862-47ae-b4a0-4b9c496b5b54
A collection of python and bash scripts to implement, train and deploy a generative adversarial network for population genetic inferences.

The networks have been tuned to be deployed to genomic data from Anopheles mosquitoes. However, the general framework can be applied to other species.

It requires the input data to be in Variant Call Format (VCF) format and the simulations need to be in msprime format.
Publication date: 2023-12-08
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More information

View numbers valid from 08 December 2023 Download numbers valid from 20 June 2024 (information prior to this was not collected)

Formats

Python scripts, Bash scripts, R script

Provenance & quality

The methodology can be applied to up to two populations at the same time. The code uses the keras python package and the scripts have been tested via simulations. Inferences were tested using simulations with known output, and the power to infer the ground truth was recovered. Simulations can be performed using msprime or SLiM.

Licensing and constraints

This model code is available under the terms of the Open Government Licence

Cite this model code as:
Pui, C.S.; Fumagalli, M.; Mathieson, S. (2023). Python code for building and training a generative adversarial network for demographic inferences from genomic data. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/3ae572f6-4862-47ae-b4a0-4b9c496b5b54

Correspondence/contact details

Fumagalli, M.
Queen Mary University of London
 m.fumagalli@qmul.ac.uk

Authors

Pui, C.S.
Queen Mary University of London
Fumagalli, M.
Queen Mary University of London
Mathieson, S.
Haverford College

Other contacts

Rights holder
Queen Mary University of London
Custodian
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk

Additional metadata

Topic categories
environment
Keywords
demographic inference , generative adversarial network , population genetics
Funding
Natural Environment Research Council Award: NE/X009637/1
Last updated
06 January 2025 09:24