Is fastq necessary for qiime2

I do not have sequence raw data,only own fasta data which has been removed the primers、low quality base and barcode. In this case How can i start qiime2 with fasta.

Hi @sumujin1! Unfortunately QIIME 2 doesn’t support importing FASTA data prior to the denoising/OTU-picking step of an analysis. There is a way to import FASTA sequences that are “representative sequences” of the features in your feature table, but denoising or OTU picking has to be performed first in order to generate the feature table.

We are currently working on supporting these “upstream” FASTA files in QIIME 2, along with OTU picking. These features should be available in the upcoming 2017.9 release, which is scheduled for the end of September. We’ll follow up here when that’s available!

In the meantime, I recommend using QIIME 1 (or another tool) to perform OTU picking on your data, and then you can import the feature table and representative sequences to continue analyses in QIIME 2.


thank you very much.


vsearch-based OTU picking, as well as “upstream” FASTA support, is now included in the 2017.9 release! There’s a community tutorial for OTU picking coming soon. :tada:


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