Circular references

You can indicate to the clc_mapper tool that you are mapping to a circular reference by using `-z' option in front of the file containing the circular genome. This option indicates that the next reference sequence to be input, using the -d option, is circular.

In the case of human genome and mitochondrial references then, the input command would look like this:

clc_mapper -o assembly.cas -d -q reads1.fasta reads2.fasta
                                                      -d -z

This will cause the mapper to map reads spanning the start point of the circular reference sequence as if they were mapped to a contiguous reference sequence. Note that the `-d' option is used twice in the example above to achieve this.

* Please note this functionality is not available for the legacy read mapper.