These are some scripts and tools that I have created and used! All of them can be found in my GitHub.
These scripts were used in: Rodríguez-Gijón A, et al. 2025. The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions.
bioRxiv (2025). DOI: 10.1101/2025.03.24.644981.
Link to the GitHub Repository: https://github.com/alejandrorgijon/competitive_mapping_scripts.
Summary: These scripts were used to estimate the relative abundance of a series of species-level clusters of Archaea and Bacteria across a set of raw metagenomic reads. These scripts help you 1) to download the FastQ files of the metagenomic reads, 2) to trim the metagenomic reads leveraging MiGA and various trimming tools, 3) to map the selected representative genomes against the trimmed metagenomic reads, 4) to estimate the number of prokaryotic genomes present on the set of trimmed reads, and 5) to estimate the relative abundance of each representative genome or species-level clusters.
Link to the GitHub Repository: https://github.com/alejandrorgijon/plada_package.
Summary: This R package was originally designed to help the user to parse metagenomic data, but it can be used across a diversity of projects and data types. To install it and use it, please check the GitHub repository indicated above.
If you would like to contact me, you can write me to alejandro.rgijon@mncn.csic.es
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