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