In version 8.1 and above, it is not necessary to select the reference sequence prior to choosing Map to Reference. Instead, the reference sequence can be chosen from within the Map to Reference setup options by clicking Choose.... This brings up a document chooser from which you can select single or multiple reference sequences from any folder in your database.
Multiple reference sequences may be selected either by choosing a sequence list containing your reference sequences, or by selecting multiple sequence documents using the Choose... button. Single reference sequences may be pre-selected prior to choosing the Map to reference... option, however when using the Choose... button, only those documents selected within the Choose... dialog will be used as reference sequences (all other sequences will be mapped).
If multiple reference sequences are selected, each read will be mapped to the sequence with the best match only, and will produce one contig per reference. Batch assemblies where each read gets mapped to each reference sequence can be done by using Workﬂows → Map reads to each reference sequence.