We have a hybridization-based, TruSeq-compatible targeted enrichment protocol from Twist Biosciences that we have been using in our lab with great success.
We would like to use the Illumina® DNA Prep, (S) Tagmentation #20025520 library prep kit with IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples) #20027213 in our current targeted enrichment workflow with as few changes as possible.
A problem we have is that the Twist Universal Blockers #100767 do not work well for these libraries, as they are not TruSeq-based.
Neither Illumina nor IDT sell their blocking oligos for Illumina® DNA Prep, (S) Tagmentation as a stand-alone product.
Has anyone found an alternative blocking solution that works well for these libraries? Do you have any other suggestions on how to improve the on-target rate in the absence of an optimal blocking solution?
For any of you that are following this question, IDT offers a Nextera-compatible blocking oligos as a commercial product now. Problem solved!
https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/blockers/blocking-oligos/blocking-oligos---p5
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