I am going to perform the 16S rRNA gene sequencing for the V3-V4 region on the NextSeq platform PE300. May I confirm if this can be adapted to QIIME2 pipeline? I did this in my previous project, but that one was performed on the MiSeq platform PE300. It worked well.
Thank you for your insight!
Illumina now sells a PE300 kit for the NextSeq 1000 and 2000, and that 600 cycle kit should be able to cover the ~450 bp V3-V4 region.
Not that the NextSeq 550 only goes up to PE150 reads.
So, which NextSeq are you using?
The PE300 kit should be able to cover V3-V4, but I have seen runs lose quality in R2.
So while they do fully cover the region, they can't join well and this causes problems.
Generally, I've had a good experience with the NextSeq, but there are always limitations.