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Old 01-14-2011, 07:39 AM   #1
UB Buffalo Bioinformatics
Location: Buffalo NY

Join Date: Nov 2009
Posts: 26
Default Demultiplexing Illumina reads

I did some searching and came up with very little about how to effectively demultiplex illumina data off the GAiix platform. Does anyone know of a good software package or workflow I could read through and experiment with? Sorry if this question has already been asked, I wasn't able to find much information though
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Old 02-16-2011, 10:17 AM   #2
Location: San Antonio, Texas

Join Date: Feb 2011
Posts: 14

Are you using your own barcodes or the Illumina multiplexing kit? The most recent version of NextGENe handles the demultiplexing of the data from the kits. I'm also trying to get it to work with CLC Genomics Workbench, but so far they aren't sorting right. Both of these programs cost $$ and I'm unfortunately not aware of free software that does it, although I'm sure it exists and someone else might know. Illumina software (CASAVA) will demultiplex data generated from their kits. It sorts into bins 1-24 (or 1-48?) but make sure to check what adapter/barcode is sorted into each bin because the numbers 1-24 don't correspond to adapters 1-24. I hope that helps!
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