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?¶
- Follow the tutorial: First Steps with ddRAGE.
- Read more about input formats.
- Read more about output formats.
- Browse a list of command line parameters.
- Take a look at the ddRAGE cookbook.