Contains scripts and programs used to generates assemblies and variants for the DSPR project
Each folder contains various data objects and scripts as described below -
rscripts : contains all R scripts used to analyze data and make figures.
Illumina: contains the output from the Illumina genotyping.
scripts: Contains scripts used to construct the variant table. All contains the variant data in tab format, prior to VCF conversion.
validation: contains the lists of randomly picked SVs that were manually inspected on the UCSC browser.
variants-raw: contains the svmu and Repeatmasker output for each strain.
variant_data: contains the variants in a custom tab separated file and a vcf file.