The first stage of the base space mapper is to create an index file for the reference sequence(s) being used. For a given reference, the index will be identical each time you run the mapping tool. You can choose to save the index file that is created during one mapping run, and then re-use the index file in subsequent mapping runs.
-n <file> / --indexoutput <file>parameter causes the index file for a particular reference set to be saved.
This reference index can be used instead of a reference sequences in subsequent mapping runs, i.e. use the name of the index file after the -d flag instead of the reference file name. If you have multiple index files, these can be entered individually as arguments to the -d flag similar to multiple reference files.
* Please note this functionality is not available for the legacy read mapper.