Core analysis tools

De novo assembly and mapping reads to reference sequences form the core tools of CLC Assembly Cell. These tools can be accessed using the following commands:
De novo assembly.
Used for mapping reads to a reference sequence.
The read mapper included in earlier versions of CLC Assembly Cell. This tool is for mapping sequencing reads from the SOLiD color space platform to a reference sequence.

The output of a de novo assembly is a set of contig sequences in fasta format.

The output of read mapping tools is a file in a special format called cas. The file extension for this file is .cas.