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simka

+# creates liste of the samples. 
+ls *subset* > temp
+#creates right format for SIMKA
+awk -v var=$(pwd) '{print "id"NR": "var"/"$0}' temp > liste
+conda activate simka-1.5.2
+### Kmersize can be optimized for the sample, default is 21, tmp files can be kept, but is not necessary. 
+[location]/bin/simka -in [liste] -out simka_out -out-tmp simka_temp -keep-tmp -kmer-size 30 -nb-cores 4 -max-reads [number]
+
+### R script to make figure
+### REMOVE FIRST ; IN CSV FILES!!!!
+a<-as.matrix(read.table("file.csv",sep=";",header=T))
+#list
+rownames(a)<- c("samplename1","samplename2")
+colnames(a)<- c("samplename1","samplename2")
+#plot
+heatmap(a,trace="none", Rowv=F)
+#print plot
+pdf("name.pdf", width=15, height=15)
+heatmap(a,trace="none", Rowv=F)
+dev.off()