How to use DADA2 with QIIME2 ?


I write to you for invocation of DADA2 using qiime2. Could you mention the commands lines and the input files required to perform this task ?


HI @M_F,

Have you checked the q2-dada2 documentation? Usually the help text is the best place to tell you about input files, outputs, and the parameters you're working with.

Certain functions are easier to use when you have an example, for dada2, I might look at the Moving Pictures or the Atacama soil tutorial data. However, just because a command isn't in a tutorial doesn't mean the command doesn't exist; again, start with the plugin docs.


1 Like

HI @jwdebelius,

Thanks. I checked the documentation. Shall i use both commands :
qiime dada2
from qiime2.plugins import dada2
Which one can i use ?
By the way, the sequences are already demultiplexed. I have actually a seqs.fna input file i generated from this one seqs.qza file using the following command
qiime tools import
--input-path seqs.fna
--output-path seqs.qza
--type 'SampleData[Sequences]'
after that i generated the following files : table.qza + rep-seqs.qza by dereplicating sequences.
Can i use the last output files table.qza + rep-seqs.qza to run DADA2 ?

Hi @M_F,

Usually I recommend sticking with one way of accessing QIIME. It looks like you're already using the command line, so I would use the command line version: qiime dada2.

I also strongly recommend looking at the steps that were taken witth the demultiplexed sequences in the tutorials I linked above; do they dereplicate? Given that dada2 runs directly on fastq sequences for error profiling, why might or might not dereplicating be a good idea?


Hello @jwdebelius ,


1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.