How to set the minimal merge length in Deblur denoise-16S?

I tried to merge some paired-end sequences and set the minimal merge length to 200bp, but got confused if that is an possible in the Deblur denoise-16S module. Basically, I want to retain merged sequence of all lengths but remove those forward and reverse sequences that have less than 200bp overlaps.

Hi @Du_Niu,
Good question! It looks like denoise-16S does not have a minimal merge length option. In fact, denoise-16S does not actually handle paired-end read data unless if it has already been joined (it accepts paired reads as input but I believe it only processes the forward reads if those reads are not joined).

Use qiime vsearch join-pairs to join your paired-end reads, and use the minovlen parameter to adjust minimum overlap. The output of that command will contain joined reads, which you can then input to denoise-16S.

I hope that helps!

Great, just tried and it works~ thanks a bunch. A follow up question, is there a way to specify the sliding window size like in q-score filter?

It does not look like it… but deblur should be run after using q-score anyway to do a first-pass filter. So use this workflow:

  1. join with qiime vsearch join-pairs
  2. first-pass filter with qiime quality-filter q-score-joined
  3. deblur

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