Hi,
I am using Qiime2/2019.1. I am new to this kind of work. However, I managed to get to the step of retrieving sequences table (table.qza after running qiime dada2 denoise paired command).
I am working on specific organisms, and would like to find a command that compare sequences to a reference (or a group of reference ) sequence and pull them, after indicating a similarity threshold. What I am asking is the exclude_seqs_by_blast.py command that used to be on QIIME 1.
Is there a similar command for qiime2/2019.1 (installed through singularity, not conda). I have tried looking into previous questions, but the most recent one was 2017 where Qiime2 didn’t have that command yet.
Thanks for the help
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Good afternoon @Seifeddine_Ben_Tekay,
Welcome to the Qiime 2 forums! Glad you are upgrading from Qiime 1 to Qiime 2! 
Qiime 1 'scripts' have been replaced by Qiime 2 'plug-ins'. You can find a list of plugins for the newest version of Qiime here:
https://docs.qiime2.org/2019.7/plugins/available/
Or here for the version of Qiime you have installed: Available plugins — QIIME 2 2019.1.0 documentation
May I suggest, qiime quality-control exclude-seqs
Good luck! 
Colin
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