Double digest restriction-site associated DNA (ddRADseq), is a variation on the RAD sequencing protocol, which is used for SNP discovery and genotyping. State-of-the-art open source analysis pipelines like Stacks can perform an in-depth analysis of RADseq data.

Pros:

• No reference genome is required
• Relatively inexpensive, compared to whole-genome sequencing
• The degree of genome coverage can be adjusted by selecting various restriction enzymes

Cons:

• There can be gaps in the genome coverage
• Requires high-quality DNA