Map Reads to Reference

Read mapping is a very fundamental step in most applications of high-throughput sequencing data. The CLC Cancer Research Workbench includes read mapping in several other tools (e.g. in the RNA-Seq Analysis), but this chapter will focus on the core read mapping algorithm. At the end of the chapter you can find descriptions of the read mapping reports and a tool to merge read mappings.

There are two different versions of the core mapper: one for color space data, and one for base space data. At 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.