Acanthamoeba castellanii genome assembly and infection by Legionella pneumophila

Data associated with the publication "<em>Regulation of the Acanthamoeba castellanii genome upon infection by Legionella pneumophila</em>". The record contains 4 archives, each associated with a github repository. 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. <strong>Hybrid genome assembly:</strong> Genome assembly pipeline code and output data used for the assembly of 2 <em>A. castellanii</em> 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 <strong>Genome annotation:</strong> Genome annotation pipeline used for functional annotation of <em>A. castellanii</em> strains C3 and Neff, and associated output files. Github: https://github.com/cmdoret/Acastellanii_genome_annotation Archive: Acastellanii_genome_annotation.tar.gz <strong>Genome analyses:</strong> Code and data related to general analyses of genomic properties of <em>A. castellanii</em> strains C3 and Neff. Github: https://github.com/cmdoret/Acastellanii_genome_analysis Archive: Acastellanii_genome_analysis.tar.gz <strong>Infection analyses:</strong> Code and data related to the analysis of structural changes in the <em>A. castellanii</em> C3 genome during infection by <em>L. pneumophila</em>. Github: https://github.com/cmdoret/Acastellanii_legionella_infection Archive: Acastellanii_legionella_infection.tar.gz <br>