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Crude AMR database harmonisation

We need a quick way to compare results between different AMR databases While there are better ideas of dealing with this problem more robustly (...speak to me about genomically-informed nomenclature normalisation), for mapping AMR databases (NCBI AMR, ResFinder, SARG, DeepARG, MEGARes, ARG-ANNOT) to CARD's ARO:

  • Download these AMR databases

  • Run them through RGI

  • Using hits, create a mapping of each ARG to the ARO

  • Highlight any situation of no hits/disconnect for manual curation

Running

Run the following commands in your terminal.

conda env create -f env.yml
conda activate crude_harmonisation
bash crude_db_harmonisation.sh

Output mapping can be found at resfinder_ncbi_sarg_deeparg_megares_argannot_ARO_mapping.tsv

Statistics

Proportion of genes mapped for each database.

argannot        0.996
deeparg         0.976
megares         0.950
ncbi            0.969
resfinder       0.976
resfinder_fg    0.983
sarg            0.978