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 a special mode for reads longer than 500bp. It is possible to mix sequence lists with reads that are shorter and reads that are longer than 500bp for the same mapping. In this case the appropriate mapping algorithm will be applied to each of the sequence lists.

The Map Reads to Reference tool does not support reads longer than 100.000bp and is not recommended for Oxford Nanopore reads.