A repository for the analysis involved in "Evidence for widespread class II microcins in Enterobacterales genomes"
Below are instructions for reproducing the analysis to identify microcins in Enterobacterales genomes. The two most important components are to have cinful installed and to download the genome assemblies.
Documentation on cinful can be found at https://github.com/wilkelab/cinful
This repository contains the accession numbers and descriptions of all genome assemblies used in this analysis. There is more than one way to retrieve these files. The easiest is with ncbi-genome-download.
The data are split into three groups. The first is the E. coli pan genome from Touchon et al. (2017). Second are genome assemblies from Enterobacteriaciae from species in GTDB that have at least 20 assemblies per genus. Finally, there is a representation of one assembly per species from other Enterobacterales.
This repository includes final output from the cinful pipeline. These final output files were analyzed to generate the figures for the paper. The analysis for each figure is stored in full across separate jupyter notebooks.