Low Diversity Libraries on NextSeq

[nangel]

Has anyone run low diversity libraries on the NextSeq500? Can you compensate with a certain amount of PhiX or is it still better to run the libraries through the MiSeq multiple times to get the read number per sample that we need?
Thanks!

[ScottC]

We have seen quite poor performance on the NextSeq with low diversity libraries. We used up to 50% PhiX with little/no improvement... that being said, the low diversity libraries that we have tried are extremely low diversity (much lower than, say, 16S or standard amplicon sequencing). Ask Illumina for their technote, though, which seems to suggest that it can be done.

[GA-J]

Ask about spacer-primers. It may help you out.

[nucacidhunter]

Check out Illumina’s support bulletin titled: Best Practices for Low Diversity Sequencing on the NextSeq System.

[tom viaene]

16S pools on NextSeq vs HiSeQ

Hi, I previously run 16S pools on a MiSeq successfully. However, i have a high number of samples that i want to run using double indexing, PE150. What is the best platform to use, NextSeq or HiseQ

[nucacidhunter]

That depends on the read length required. HiSeq output would be higher because it needs less PhiX spike-in than NextSeq and also there is option of 2x250 on Rapid chemistry.