Fig. 7

Programs (i.e. black letters) and commands (i.e. grew letters) implemented in the ‘VARCall’ workflow aiming to call single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels). The scripts referring to alignment against reference genome (i.e. ‘BAMmaker’), variant calling (i.e. ‘VCFmaker_SNP’ and ‘VCFmaker_INDEL’), variant combination (i.e. ‘SNP-INDEL_merge’), pairwise distances (i.e. ‘VCFtoMATRIX’), variant concatenation (i.e. ‘VCFtoFASTA’), pseudogenome assemblies (i.e. ‘VCFtoPseudoGenome’), and report about breadth and depth coverages (i.e. ‘reportMaker’) were written with Python 2.7 and are invoked by the driven script ‘VARCall’ (i.e. black arrow). The script ‘BAMmaker’ is performed for each genome (i.e. circular arrow)