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Old 07-26-2017, 12:49 PM   #106
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Originally Posted by pmiguel View Post
The recommended method to detect an index swap is to use "Unique Dual Indexes". With these you don't use the same i7 index in multiple pairs. A given i7 index always goes with a fixed i5 index for the run. Then if you detect an i7 index with any i5 index other than its pair, you know an index hop has occurred and the reads are discarded.

This will remove all index hops the result of a single recombination event. It will also remove nearly all the double recombinations. So true index hops should be largely detectable.

As to what causes index hopping, I don't think that Illumina is sure. They seem mainly to have a list of "best practices" to use to lower their frequency.

I haven't looked in detail at the process of exclusion amplification either. But I presume that it involves some non-flowcell-tethered PCR amplification.

Okay, this is interesting and jives with their basic premise. This is also contradictory to their NEXTERA i5/i7 design wherein Index codes are re-used multiple times.
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