SABvsIE Files

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## README ##
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The downloaded link consist of a ZIP file containing all code used and all input- and intermediate files, in this format:

-meta_data_sheet.txt
-meta_data_sheet.xlsx
-Outputs
	-Assembled_files
		-all assembled files
	-Kmer_output
		output from the python k-mer script
	-NASP_output
		-output and intermediate files from NASP (some of these files are large)
	-reference sequence used for NASP and trams
	-Roary_output
		-output and intermediate files from Roary (Prokka annotation files are not included)
	-Sliding_window_nonCore_output
		-intermediate files from sliding window analysis
	-Trams_output
		-Output and intermediate files from Trams
-R_code
	-R code used split into analysis, ordered by number used in paper
	-iTol
		-recipes used for iTol, to add colors, groups, text etc.
	-python scripts (to count k-mers)


Be aware that some of the output files are large (e.g. master.tsv is 4.4GB)





###### How to run scripts ######

These are the scripts used in the paper, separated by analysis. This means that some scripts contain both the bash and R code used for a specific analysis. Because of this, the files are not executable, but have to be opened, and copy-pasted into terminal/R to be executed. Furthermore, the scripts are not generalized, meaning the scripts work for this particular dataset, but not necessarily on a different dataset. The biggest limit is that samples have to be sorted to first contain all samples from one state, then all samples from the other state. If the samples are mixed, the scripts will not work. This is the case for both nasp- and roary output. 

As one of the first commands, the input file is read. To run on our data, be sure to be in the folder "SAB_vs_IE_code_and_data" (root of the zip file). For other input, change the file in the read.table command.
The next line contain the number of samples per state, change here for other inputs, remember check that samples are sorted per group, and which group listed first in the input table. 


Software used, but not made by us, e.g. NASP, Trams, Prokka, Roary, is not included in the ZIP file, and must be downloaded separately.