Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa

Similar Threads
Thread Thread Starter Forum Replies Last Post
low Q30 in index, miseq v3 600 cnano Illumina/Solexa 3 06-05-2019 01:43 PM
Miseq dual index Read1 (i7 index) problem? Min Jung Lee Illumina/Solexa 4 01-08-2018 12:22 PM
How to mix single index and dual index TruSeq libraries pmiguel Illumina/Solexa 31 05-24-2017 04:10 AM
Pooling TruSeq (single index) and Nextera XT (dual index) in one MiSeq run? Carosmile Sample Prep / Library Generation 1 05-16-2017 02:13 PM
Dual-index vs single index Ingeneious Illumina/Solexa 4 01-19-2015 12:22 PM

Thread Tools
Old 02-18-2019, 02:41 AM   #1
Junior Member
Location: Northern Ireland

Join Date: Feb 2019
Posts: 1
Default Tandem dual index- low Q30 for index 2


While reading up about index hopping, I came across the Illumina whitepaper ( which states that unique dual indexes help to mitigate this.

While reading another paper about index hopping (, where the authors used dual-matched indexes, they mention an online post by Illumina ( which says that distinct dual indexes work better than tandem dual indexes. Illumina present data showing how tandem dual indexes have a low Q30 for the index 2 read in comparison with distinct dual indexes and data also which shows a ‘T overcall / A undercall’ phenotype for the tandem design. However, the authors of the dual-matched index paper did not find the reduced Q30 scores reported by Illumina.

So my question is why would using a tandem index affect the Q30 score for the second index read? I don't understand how data from the first index read would affect the data generated during the second index read?

Thanks in advance for any insight!
juliar is offline   Reply With Quote
Old 02-18-2019, 09:25 AM   #2
Senior Member
Location: US

Join Date: Dec 2010
Posts: 452

The results do vary by sequencer (the Hiseq 4000 is not - or only minimally - bothered by dual matched indices); the NovaSeq OTOH can tank with these. Likely library insert sizes can also play a role.
The MiSeq and NextSeq also have no troubles with dual matched indices.

The clustering chemistry seems to be different on the NovaSeq but I have no idea what causes the problems.

Last edited by luc; 02-18-2019 at 09:28 AM.
luc is offline   Reply With Quote

index, q30, tandem, unique

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:26 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO