A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids

Repository for the scripts used to perform a comparative study of pan-genome methods, manuscript published in Microbial Genomics. If you use the code, please cite:

@article{baumanniipangenome2021,    
  title={A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids},
  author={Urhan, Aysun and Abeel, Thomas},
  journal={Microbial Genomics},
  volume={7},
  number={11},
  year={2021},
  publisher={Microbiology Society},
  doi={https://doi.org/10.1099/mgen.0.000690}
}

The scripts are essentially wrap-arounds to run our comparative study, the individual methods belong to their corresponding developers. So please refer to their repositories to confirm how to cite their work.

1. Roary (v3.13.0)
2. Ptolemy (v1.0)
3. PPanGGoLin (v1.0.13)
4. PIRATE (v1.0.3)
5. Panaroo (v1.1.2)
6. GOATOOLS (v0.9.9)

createSA.py and runGOE.py were both written in python (3.7), and the 'comparativeStudy.sh' is a bash script that includes the commands we ran to perform our comparative study.