Getting Started with ddRAGE

What is ddRAGE?

ddRAGE is a simulation tool for double digest restriction site associated DNA sequencing data. With one run of ddRAGE you can create a set of FASTQ files with ddRAD reads and the results expected from an analysis of these reads.

How does ddRAGE work?

ddRAGE simulates a set of independent loci without using a reference genome. Each individual can show one of three different types at each locus: common, dropout, and mutation. The simulated effect is annotated in the name line of the generated FASTQ files and written to a ground truth file (in YAML format).

For a detailed explanation of the simulation, please take a look at the paper and its supplement.

What to do next?