Too many unique sequences


I just wanted to know how many unique sequences are “too many”. I am using some data of my own now, and I have 2 million unique sequences. Of course, this is causing troubles with the following OTU analysis, basically I so not have enough space in my drive to store 300 + GB of data. Any clue why I would have so many unique sequences? I did all the pre processing following the SOP before getting to the OTU section. In advance, thanks!


What region are you sequencing and what chemistry are you using? What was the % reads passing filter?

I am using the 16S V4 region. It was a MiSeq Illumina run, 2x250. %Q>30 for Read 1 = 86.55. %>Q30 for read 2 = 65.64.

Hey Elliston,

That second read looks pretty poor. You might want to follow up with your sequencing provider and see if they can’t get you better data.