Map Reads to Reference

Read mapping is a very fundamental step in most applications of high-throughput sequencing data. CLC Genomics Workbench includes read mapping in several other tools (such as in the Map Reads to Contigs tool, or for 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.

In addition, the mapper has special modes for handling PacBio reads and reads longer than 500bp. Before the Map Reads to Reference tool starts to map the reads, it checks the input sequence list(s) to decide on the mapping algorithm to use:

It is possible to mix sequence lists that have the platform field of the read group "PacBio" with sequence lists that have a different read group for the same mapping. In this case the appropriate mapping algorithm will be applied to each of the sequence lists.