I don’t run a sequencing core, but I’ve worked closely with folks who own both the Illumina MiSeq and NextSeq 550.
The Illumina MiSeq and NextSeq 550 are really different machines.
I think the MiSeq is commonly used for 16S analysis because of it’s longer reads (300 bp, paired end) and sweet spot for an amplicon study. With ~300 barcodes and 15 Million reads per run, you would hopefully get ~50k reads per sample, which is a reasonable number for an amplicon study.
While the NextSet 550 offers many more reads, the EMP primers still just offer ~300 barcodes. (Other barcoding schemes let you process more!) Plus, it might be preferable to sequence a longer region for better taxonomic resolution, than simply increase read depth. 300 bp > 6 million reads per sample
Oh, and buying one MiSeq is less expensive than buying one NextSeq 550
But the NextSeq 550 is super reliable, and the MiSeq is ~11 years old.
- cheap machine, long reads, low depth, delicate
- expensive machine, shorter reads, greater depth, reliable
Are you planning to buy one of these machines, or learn more about the platforms before buying a run from a company or sequencing core?
P.S. If someone on here does run a sequencing core, please correct my mistakes! I would love to learn more about the NovaSeq, as I’ve not worked with one before!