Demultiplexing using variable-length barcodes

[id0]

Is there a tool for demultiplexing using variable-length barcodes? If it makes any difference, the barcodes are within the read, not a separate read.

My personal solution would be to demultiplex in multiple steps, starting with the longest barcodes. Is there a better option? There are a lot of demultiplexing tools. Surely one of them supports barcodes of different lengths.

[JackieBadger]

you can use jMHC.
You will have to make separate de-multiplexing passes though.
The program is a lot faster on Mac than PC/Ubuntu for some reason but is easy to use and produces good output excel files.

Also, depending on your data set size, you may need to open jMHC/java from the terminal - allocating more RAM. I can get though ~ 2M reads in a couple of hours