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# amr_mice_cosmic
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## Here in lie the scripts and methods used to generate data for the two following projects
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    -   mice-AMR study
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## A brief description of the analyses is below:
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    - Snakefiles: snakemake-based scripts for launching IMP3, MAG taxonomy and quality analyses and integron coordinate retrieval 
    - config: folder containing all config files required for Snakefiles
    - envs: folder containing all conda environments, including for Rscript analyses
    - Integron_Prediction: folder including snakefile, config and supplementary scripts for integron prediction
    - scripts: folder containing supplementary scripts, including Rscripts for generating figures for the paper
    
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## Step-by-step analyses 
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- Detailed and additional information including explicitly described processing steps can be found in the [Wiki](https://git-r3lab.uni.lu/susheel.busi/intonate/-/wikis/mice_amr_analyses)