Data associated with the publication "Regulation of the Acanthamoeba castellanii genome upon infection by Legionella pneumophila". The record contains 4 archives, each associated with a github repository, and a "shared assets" archive, which contains processed files used by some repositories. The code from github repositories is embedded in each tarball, along with input and output data. Analyses are organized as independent snakemake pipelines for each part. For convenient reanalysis, genomes, annotations and merged contact maps used in the publication can be found in the `data/input` folder of Acastellanii_genome_analysis.tar.gz. The infection results are located in the `data/output` folder of Acastellanii_legionella_infection.tar.gz. Hybrid genome assembly: Genome assembly pipeline code and output data used for the assembly of 2 A. castellanii strains (Neff and C3) through a hybrid pipeline combining Illumina shotgun, Hi-C and Oxford Nanopore long reads. Github: https://github.com/cmdoret/Acastellanii_hybrid_assembly Archive: Acastellanii_hybrid_assembly.tar.gz Genome annotation: Genome annotation pipeline used for functional annotation of A. castellanii strains C3 and Neff, and associated output files. Github: https://github.com/cmdoret/Acastellanii_genome_annotation Archive: Acastellanii_genome_annotation.tar.gz Genome analyses: Code and data related to general analyses of genomic properties of A. castellanii strains C3 and Neff. Github: https://github.com/cmdoret/Acastellanii_genome_analysis Archive: Acastellanii_genome_analysis.tar.gz Infection analyses: Code and data related to the analysis of structural changes in the A. castellanii C3 genome during infection by L. pneumophila. Github: https://github.com/cmdoret/Acastellanii_legionella_infection Archive: Acastellanii_legionella_infection.tar.gz Shared assets: This archive contains processed files (genomes, annotations, Hi-C matrices, differential expression results) which can be useful for reanalysis, and are automatically pulled when executing the pipeline of some repositories. Archive: shared_assets.tar.gz