We have been running Nextera in my lab for a while now and had some great success e.g. 600x C. elegans genomes. With the release of Illumina's rapid exome kits Nextera is proving to be a versatile and useful addition to our lab tools. Unfortunately it has at least one significant weakness; the need to accurately quantify dilute DNA.
Nextera requires a precise ratio of DNA to transpososomes. Get this wrong and the libraries may not be great and might be unsequenceable.
The standard prep calls for Genomic DNA at 2.5ng/μl and the Nextera XT wants just 0.2ng/μl. We find that many users struggle to get this right for their samples. Most see an improvement if they use a good quantifiaction method and Illumina provides recommendations in the manuals. The use of a double-stranded DNA intercalating dye (we use QuBit) means single-stranded DNA, RNA and other contaminants don't confuse the readings. Nanodrop is a no no for Nextera!
Using SPRI beads to improve the protocols: I have been thinking how we might use a SPRI bead step at the start of a project to capture a very specific amount of DNA. Illumina are using SPRI for bead-based normalisation at the end of the process, so why not add it at the start?
The method is simple enough and would be much quicker for labs without fluorimetric plate readers who have to QT each sample one at a time.
We've not started testing a method yet but next time we're running a Nextera protocol we'll be giving it a go.