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Pré-Publication, Document De Travail Année : 2024

PopSize, a snpArcher module for population size change inference

Résumé

The increasing scale of genomic datasets necessitates robust and scalable tools for demographic inference, especially for non-model organisms. To address this need, we developed Popsize, a solution designed to simplify the integration and usage of common demographic inference tools within a cluster infrastructure. As a module of snpArcher, a highly parallelized variant calling pipeline, Popsize enhances the scalability and robustness of demographic analyses to make it more accessible. Popsize can run up to five of the most cited demographic inference tools in parallel, directly utilizing input from the snpArcher pipeline without requiring additional materials or setup. This integration streamlines the process, making it more efficient for users handling large datasets. Implemented as a Snakemake module within the snpArcher pipeline, Popsize is freely accessible on GitHub (https://github.com/tforest/popsize). It is available under the same licensing conditions as snpArcher, ensuring ease of access and broad usability for researchers in the field.
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Dates et versions

hal-04599797 , version 1 (04-06-2024)

Identifiants

  • HAL Id : hal-04599797 , version 1

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Thomas Forest, Swan Portalier, Camille Steux, Timothy B Sackton, Guillaume Achaz. PopSize, a snpArcher module for population size change inference. 2024. ⟨hal-04599797⟩
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