Dual indexing on NextSeq

bryanbriney · 06-10-2014, 09:49 AM

Illumina announced updates to the Prep tab in BaseSpace that enable a couple of missing features for NextSeq users -- dual indexing and custom indexes. Also, we just received some new Mid-output kits and the Accessory Box now contains an additional 'dual index primer' reagent, which is to be added to well #18 when performing a run with dual indexes.

http://blog.basespace.illumina.com/2...pace-prep-tab/

TonyBrooks · 06-19-2014, 07:59 AM

Yep. They've changed the way dual indexing is done on on the NextSeq. BP10 is the primer to read the i5 index and needs to be added to #18 for all dual index runs. Our FAS told us paired end turnaround is carried out even on single read conformations in order to read the second index. The reason they switched is because the lack of dark cycles before the index read improves the read quality (less (pre)phasing) and therefore gives better assignment. The software must reverse compliment the i5 read because it's now reading from the other direction.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
A first look at Illumina’s new NextSeq 500	AllSeq	Vendor Forum	111	03-12-2020 03:25 AM
Dual indexing construct for MiSeq - where to put the barcode for index2?	Vinz	Illumina/Solexa	50	12-12-2014 03:19 PM
no dual indices on NextSeq 500 (yet)	SeqNerd	Illumina/Solexa	9	10-20-2014 12:06 PM
Custom amplicon sequencing with dual indexing	tickseq	Illumina/Solexa	2	06-27-2013 10:46 AM
96 or 384 Nextera-style dual indexing	pmiguel	Illumina/Solexa	3	06-27-2012 10:49 AM

06-10-2014, 09:49 AM	#1
bryanbriney Junior Member Location: San Diego Join Date: May 2014 Posts: 8	Dual indexing on NextSeq Illumina announced updates to the Prep tab in BaseSpace that enable a couple of missing features for NextSeq users -- dual indexing and custom indexes. Also, we just received some new Mid-output kits and the Accessory Box now contains an additional 'dual index primer' reagent, which is to be added to well #18 when performing a run with dual indexes. http://blog.basespace.illumina.com/2...pace-prep-tab/

06-19-2014, 07:59 AM	#2
TonyBrooks Senior Member Location: London Join Date: Jun 2009 Posts: 298	Yep. They've changed the way dual indexing is done on on the NextSeq. BP10 is the primer to read the i5 index and needs to be added to #18 for all dual index runs. Our FAS told us paired end turnaround is carried out even on single read conformations in order to read the second index. The reason they switched is because the lack of dark cycles before the index read improves the read quality (less (pre)phasing) and therefore gives better assignment. The software must reverse compliment the i5 read because it's now reading from the other direction.