Is it safe to use Nextseq in 16s sequencing?
I have some ocean samples to sequence the 16s, however, due to some infrastructure limitations, I can only use a Nextseq for sequencing. Is it okay to do that? What are the best regions to use in this case? Can I use the same V3-V4 regions used in Miseq? I looked for articles that had already done this, but I found only two, that didn’t write about the difference or why they chose Nextseq, so I’m not so confident to do that.
The articles that I mentioned:
Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls - https://doi.org/10.1038/s41598-018-27314-3
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome - https://doi.org/10.1371/journal.pone.0212474
Thanks a lot!