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Old 06-20-2016, 02:32 AM   #1
Location: Slovenia

Join Date: Mar 2015
Posts: 19
Default Truseq libray spike-in into Nextera library run


In our lab we routinly perform exome sequencing with Nextera kits on Mi/HiSeq platforms.
In my experiment I want to sequence libraries made with Truseq DNA PCR-free LT kit and enriched with custom IDT xGen probes.
Since the targeted sequence is relatively small, or me it would be the cheapest to add/spike this library into the runs we perform on regular basis (Nextera).

I found this on Illumina's FAQ:
Can I run TruSeq HT libraries with Nextera libraries on the same lane or same flow cell? Are the indices the same or different?

Illumina does not support, and strongly advises against, running libraries prepared by different sample prep kits in the same lane of a flow cell. We do support running libraries prepared by different sample prep kits in different lanes of the same flow cell or spiking in llumina PhiX control library in the same lane as any user-prepared libraries. If different library types are run in different lanes, Dual Index Recipes and the Dual Index Primer Box must be used. The indices between TruSeq HT and Nextera are unique and not shared. Please see appropriate sample prep user guides for index sequences.

It is for the HT version of the kit, but it also says that dual indexing is necessary. Tru-seq pcr-free LT kits are single index. Does that mean I absolutely can't do the spike in? What are your experiences?

If anybody has any experience with mixing libraries made by different protocols on Illumina platroftm, can he/she please comment.

Thank you!
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