Which strategy for taxonomy assign

[Nicholas_Bokulich]

Hi @lindd,

@lindd

I also want to want to compare qiime2 suggested pipeline (denosing by DADA2) with the pipeline previously used in qiime1 for curiosity.

DADA2 vs. OTU picking performance has been benchmarked in the dada2 publication.

I would strongly recommend sticking with denoising if you are just getting started in QIIME2 (as opposed to transitioning from QIIME1; many transition users are comfortable with OTU pipelines and/or need to process data for comparison to older results, but that does not sound like the case here)

If you do want to perform OTU picking in QIIME2, several methods (mirroring those supported in qiime1) are available in the q2-vsearch plugin. These should be accompanied by rigorous sequence quality filtering (see below) and chimera checking.

@lindd

Another thing I am confused is there is a trimming of sequence step in qiime2 tutorial but not in qiime1.

Sequences are usually trimmed in qiime1 during demultiplexing. DADA2 trims sequences to a set length but this is manually set by the user — qiime1 actually performs more what it sounds like you are describing, trimming sequences programmatically wherever quality begins to drop below a defined level (and hence sequences are of different lengths post-filtering)

@lindd

Or any way/method we can use to trim sequence by quality score like we did in qiime2 but not involving another processing?

qiime1-style quality filtering can be performed with the q2-quality-filter plugin. This step is not necessary if you are using DADA2, but is needed if you are using deblur or OTU picking. If passing these inputs to OTU picking in particular, see here for recommended parameter settings for q2-quality-filter (the defaults are minimal and more useful for following with q2-deblur for additional quality filtering).

I hope that helps!