A repository containing the data and programs for studying CRISPR-Cas and AMR genes in healthcare-related pathogens
To download/visualize identified CRISPR-Cas systems, please go to CRISPRone website.
What's included in this repository:
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Data
- tables/: tables showing the presence of CRISPR-Cas systems and the number of predicted AMR genes in the different isolates of each species
- data/amrplus_eskape.csv.gz: predicted AMR genes in all pathogen isolates
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Programs
- CRISPR-AMR-test.ipynb: a python notebook for statistical testing if CRISPR-Cas containing isolates tend to have fewer AMR genes
- lib/build_spacer2mge_network.py: script that takes spacer blast outputs and spacer cdhit outputs and constructs a MGE:spacer network
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Example: build MGE:spacer network
python lib/build_spacer2mge_network.py \\
--phage blast_output/example_phages.filtered.derep.m8 \\
--plasmid build_network_example/blast_output/example_plasmids.filtered.derep.m8 \\
-c build_network_example/cdhit_out/example_cdhit0.85.clstr \\
-o build_network_example/example.gml
Reference: Comparison of CRISPR–Cas immune systems in healthcare-related pathogens" by Kate Mortensen, Tony Lam and Yuzhen Ye (submitted)