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.
- Roary (v3.13.0)
- Ptolemy (v1.0)
- PPanGGoLin (v1.0.13)
- PIRATE (v1.0.3)
- Panaroo (v1.1.2)
- 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.