Script for open_reference_OTU picking in QIIME2

Hi, I have the sequence file (paired and demultiplexed) from QIIME1. When I am doing the open reference OTU picking in QIIME2 I am getting an error “command not found”. I was wondering if anyone can help me with the script for open reference OTU picking in QIIME2?
Thanks in advance.

Hi @Nida,
A tutorial for OTU picking in QIIME2 is here.

If you are new to QIIME2, you should check out our documentation to get started. The tutorials at that link — particularly the “moving pictures” and importing data tutorials will help you transition from qiime1 to QIIME2. QIIME2 is a whole different beast! :hedgehog:

I hope that helps!


I checked it the link that you proposed to see the OTU picking with QIIME2, but I saw only instructions for “de novo” and “close_reference”.

Anyone knows how to do “open_reference_OTU_picking”?

Thank you very much for your help in advance!

Hi @MMC_northS,
Instructions for open-reference OTU picking are here.

All available plugins are searchable on the QIIME2 website.

I hope that helps!

Hi, Nicholas,

Yes, the link is so useful for me and along with the answers in the other chat,
"Questions about Open Reference OTU Picking " between you an other girl. I am trying to understand the transition between QIIME1 and QIIME2 and there I have found really useful answers about what possible orders or ways i can use to analyze my data, so thank you very much!.

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