How to merge rep-seqs from 3 runs after dada2?


I have three Illumina Miseq sequencing runs with different samples in each for the same project. I imported and processed them separately in QIIME2 through the dada2 step. The resulting feature-tables were merged according to directions found in the forum. However, I cannot find instructions on how to merge the rep-seqs files. Is there a way to merge these in QIIME2 and if so, how please?

Thank you,


Hi @kmkalanetra!

I think you just need the qiime feature-table merge-seq-data command.

We’ve got a tutorial that specifically addresses merging multiple runs which you may be interested in.

P.S. You can add --help to any command (or partial command) to learn more.
(for example I ran qiime feature-table --help to remember the exact command you needed)


Hi Evan,

Thank you so much! I googled and searched the forum, but didn’t see this. Your answer is just what I needed. So simple.


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