gDNA library prep kit for NovaSeq 6000?

[JakobHedegaard]

Going to have a NovaSeq installed soon and wonder which library prep kits are most optimal for human gDNA? We are going to use the libraries for both WGS and for capture (exome/panels). Index hoping must of course be handled by the library kit.
Thanks, /Jakob

[kwaraska]

novaseq

We use Illumina UDI for indexes as there are 96 choices so you can run a large number on the NovaSeq. In this way, if the forward index does not match the reverse index, you can discount the read as index hopping.

Depending on how many exomes you run, you may want to upgrade to the lane loader for the S4 flow cell so you can run as 4 lanes. That will give you more flexibility to run genomes and exomes on the NovaSeq. Otherwise, at standard coverage metrics, you will need a 384 index set.