lpxC diversity in published E. coli datasets

Data and scripts for analysing the diversity of the gene lpxC in public Escherichia coli datasets on NCBI. Analysis provided linked to paper [1].
Scripts provided 'as is'. Please get in touch if you have any questions about using them (see contact details in README.md).

Analysis.zip - zipped archive containing data and scripts for the analysis of lpxC sequences. See README.md for more details.
Assemblies.zip - combined assemblies from three datasets for n=X isolates (combination of new assemblies from short-reads on NCBI and existing NCBI assemblies). Also contains short script for identifying lpxC in the assembly and extracting sequence with blast.assembly-pipeline.sh - example assembly script used to trim and assemble short reads from NCBI SRA.
[1] Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition. Pramod K. Jangir*, Qiue Yang*, Liam P. Shaw, Julio Diaz Caballero, Lois Ogunlana, Rachel M. Wheatley, Timothy R. Walsh, and Craig MacLean.
* = equal contribution