Skip to content

Quick dirty way of mapping ResFinder(FG), DeepARG, SARG, and NCBI AMR databases to CARD's ARO

License

Notifications You must be signed in to change notification settings

BigDataBiology/quick_amr_db_harmonisation

 
 

Repository files navigation

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

About

Quick dirty way of mapping ResFinder(FG), DeepARG, SARG, and NCBI AMR databases to CARD's ARO

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • Python 52.3%
  • Shell 47.7%