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This repository contains command lines, configuration files and key output files associated with this manuscript:

Genome sequence data for 61 isolates of Xanthomonas campestris pv. campestris from brassica crops in Serbia. Tatjana Popović Milovanović, Shannon Greer, Renata Iličić, Aleksandra Jelušić, Daisy Brown, Mikaeel Hussain, Jamie Harrison, Murray Grant, Joana Vicente and David John Studholme.

Submitted to the Open Access journal Access Microbiology.

A preprint of the manuscript is available here: https://doi.org/10.1099/acmi.0.000870.v2.

  • Command lines for obtaining the genome sequences from NCBI databases are here.
  • Command lines for obtaining a reference genome sequence for PhaME are here.
  • Command lines for Unicycler genome assemblies are here.
  • Command lines and configuration file for PhaME are phylogenetic analysis here.
  • Results of the PhaME phylogenetic analysis are here
  • Command lines and results of CheckM analysis are here
  • Command lines and results of QUAST analysis are here.
  • Command lines and results of ANI analysis with FastANI are here.
  • Command lines for fixing start sites of circular plasmid sequences, in preparation for alignment, are here.
  • Command lines and results of BLASTN searches of genome assemblies against plamid sequence are here.