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Old 10-19-2017, 05:48 AM   #1
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Default index diversity on MiSeq

Can I run 2-3 index combinations on MiSeq? I'd be using Nextera XT DNA sample preparation index kit and MiSeq v2 reagent kit. If I select index pairs with maximum diversity, might it be safe to try?
What would insufficient index diversity look like, and is the data retrievable in the worst case scenario?
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Old 10-19-2017, 09:22 AM   #2
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If you use the standard indexes it should be fine. Illumina has a white paper somewhere that recommends specific combinations of indexes depending on number of samples you are pooling.
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Old 10-19-2017, 01:59 PM   #3
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And here is the link for Nextera low plex pooling guide:
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dual indexing, index diversity, miseq v2, nextera xt indices

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