Sequencher 5.2 and later uses a multiplexing method of de novo or reference based assembly with BWA, GSNAP or Velvet. Multiplexing is quick and easy. Each DNA sample has a specific barcode associated with it. Sequencher can read these barcodes and divide the data into various files or 'bins' . Sequencher then takes the sequences in each ‘bin’ and performs the assembly or alignment for you. Sequencher’s Multiplex ID can be used with single or paired-end data. For paired-end data, each read in the pair must have the same barcode at the 5’ end to be recognized as a pair. You can use the Tablet viewer to view the results of the multiplex assembly or alignment.
For more information on Multiplex ID, check out the Multiplex IDs with BWA, GSNAP, and Velvet Tutorial.