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Old 09-28-2017, 09:59 PM   #6
luc
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Location: US

Join Date: Dec 2010
Posts: 451
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The first indexed adapter designs were actually "in-line" indices.
Today they are only rarely used because of the already mentioned reasons and:

- the first five bases can be critical for the cluster registration and the "calibration" of the basecaller ; these sequences should be of high diversity and not low diversity sequences like barcodes. There were frequently problems with the "balancing" of these barcodes
- in-line barcode adapters are more expensive to generate since you need two complementary oligos for each index; not so for TruSeq and Nextera style adapter oligos. Thus, the latter allow also dual-indexing.
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