There are two different versions of the core mapper: one for color space data, and one for base space data. At http://www.clcbio.com/white-paper you can find white papers with detailed benchmarks and descriptions of both algorithms.
The following description focuses on the parameters that can be directly influenced by the user.
- Selecting reads and reference
- Including or excluding regions (masking)
- Mapping parameters
- Mapping paired reads
- Non-specific matches
- Gap placement
- Computational requirements
- Reference Caching