QIIME2: denoise-16S method of Deblur plugin

Per the documentation of the denoise-16S method, the Docstring of the command describes that only forward reads are supported at this time by the method. But the demux-filtered.qza (input to 16S method and output of the first quality filtering step in Deblur) is a result of sequence filtration steps on "paired-end-demux.qza", which includes both the forward and reverse reads in the import step into QIIME - So, exactly how does this work?

I ran the following command: qiime deblur denoise-16S --i-demultiplexed-seqs demux-filtered.qza --p-trim-length 170 --o-representative-sequences rep-seqs-deblur.qza --o-table table-deblur.qza --p-sample-stats --o-stats deblur-stats.qza

It worked well and gave me no error. However, I am trying to understand if my output includes reverse reads at all.

Thank you.


Hi @aakarsharao,

As far I know. Deblur does not consider the reverse reads so your output it includes read 1 only.
You can denoise paired end reads with deblur, by joining them first, as described here:

(I suggest to perform the quality step after the joining too!)
Hope it helps


Thank you for your input @llenzi . The code worked well to join my sequences.


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