PCNE v2.0.0 validation

This repository contains all the data used to validate PCNE v2.0.0 (https://github.com/riccabolla/PCNE), and is to be used with scripts provided at https://github.com/riccabolla/PCNE_paper_script.

1. Real_data:

Real_data_reads: it contains filtered reads*

Real_data_assembly: it contains assembled genomes generated using reads in the previous folder

Platon_real_data: it contains the platon's output generated

*Reads have been taken from this work: Xiang G, Zhao Z, Zhang S, et al. Porin deficiency or plasmid copy number increase mediated carbapenem-resistant Escherichia coli resistance evolution. Emerg Microbes Infect. 2024;13(1):2352432. doi:10.1080/22221751.2024.2352432

2. Simulated_dataset:

It containts the chromosome and plasmid fasta files

Sim_50x: it contains the simulated reads

Shovill_50x: it contains assemblies generated using the simulated reads

Mobsuite: it contains mobsuite's output generated

Platon: it contains platon's output generated

3. Case_study:

Case_study_reads: it contains filtered reads**

Case_study_assembly: it contains assemblies generated using reads in the previous folder

Case_study_mobsuite: it contains mobsuite's output generated

Case_study_abricate: it contains abricate's output generated

**Reads have been taken from this work: Jian, Z., Liu, Y., Wang, Z. et al. A nosocomial outbreak of colistin and carbapenem-resistant hypervirulent Klebsiella pneumoniae in a large teaching hospital. Sci Rep 14, 27744 (2024). https://doi.org/10.1038/s41598-024-79030-w