# dspr-asm
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.
