These are the scripts that have been used for different analyses included in the Blumeria graminis f. sp. hordei DH14 genome manuscript

Filename and Analysis/Function used are below:

Figure	Filename	Comments
Figure 3C	01_Mapping_SNP_Splitstree.sh	Mapping with BWA and following the GATK pipeline with alteration suggested in the TSL workshop
Figure 3A	02_CopyNumberVariation.sh	Bash was used to generate the bed files, please also look in Final_documentation.Rmd
Figures 3,4,5	Final_documentation.Rmd	R markdown with scripts
Suppl. Figure 2,8-11	Final_documentation.Rmd	R markdown with scripts

Intermediate analysis files can be found in the folder "useful_files".

Datasets used for the analysis of the DH14 genome (annotation,assembly,SPs & CSEPs) can be found in "assembly_genome_dh14".

For questions or more information please email lamprinos.frantzeskakis [at] rwth-aachen.de