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to perform a large-scale multi-sample snip analysis the first step is to assemble your multiplex data in seekman engine to do this set up your project as usual but after adding your read files check the multiplex data option this will allow your data to be assembled as multiple samples for 454 or ion torrent data your samples will be separated using standard mid or barcode tags or custom tags that you define for illumina data read files are typically already separated out by sample so all you need to do after selecting the multiplex option is to name each sample once your multi-sample data has been assembled you can begin your analysis in seekman pro youll see that in the alignment view for multiplex data my reference sequence is shown here at the top and then i can also see the consensus sequence for each of my four samples for this example ive assembled the exomes of four individuals and you can see them listed here clicking on the triangle next to an exome name will show me the co