UPDATE: For those of you unwilling to just jump at these, we have validated all of these extended indices and have not found problems with any of the full set of 24, across 6 lanes of multiplexed Illumina sequencing. You may also be interested in edittag, which provides a more generic solution to the barcode generation problem.

The Epicentre Nextera kit comes with aliquots of barcodes that are compatible with the Illumina multiplex system. However, they only send you adapters with 12 different indices:

#Index  Name
ATCACG  IDX_1
CGATGT  IDX_2
TTAGGC  IDX_3
TGACCA  IDX_4
ACAGTG  IDX_5
GCCAAT  IDX_6
CAGATC  IDX_7
ACTTGA  IDX_8
GATCAG  IDX_9
TAGCTT  IDX_10
GGCTAC  IDX_11
CTTGTA  IDX_12

For whatever reason (HiSeq, anyone?), we may want to run a number of indexed sequences in a single sequencing run larger than 12. Thus, we want to extend the set of 12 adapters to support a larger number of samples. Skip to the results, here are the indices/barcodes that extend the set of 12:

• Extended Nextera Tags (6nt, edit distance = 2)

Now, as you'll see below, the default set of barcode IDX adapters are edit distance 2 apart from one another. I don't typically feel comfortable until barcode adapters are edit distance ≥ 3 from one another - so, if we want to extend the Nextera set (using most of the adapters provided), we can DROP IDX 1 and IDX 8 from the set of adapters that came with the kit, and then design additional adapters from the barcode sequences int the following (see below for slightly more detail):

• Extended Nextera Tags (6nt, edit distance = 3)

I didn't have tons of time to spend on this, so what you can see over at github is slightly ugly. But, it is what it is. Also, I put the Methods posted over on github to catch any changes, but the <script> formatting that you get (notice below) is not quite WYSIWYG.