# Vsearch and DADA2
**URL:** https://forum.qiime2.org/t/vsearch-and-dada2/19006
**Category:** User Support
**Created:** [March 27, 2021, 6:17am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006 "2021-03-27T06:17:08Z")
**Posts on this page:** 8
**Page:** 1
### Author:  [@suetli19](https://forum.qiime2.org/u/suetli19)
#### Post date: [March 27, 2021, 6:17am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/1 "2021-03-27T06:17:08Z")
Hi, I am processing Miseq paired-end reads (2times251bp) targeting the V3-V4 region of the 16S. I have performed cutadapt to trim out the adapter and primer sequences. And this is the quality plot:
This is the command line:
From this step onwards, I am confused on how to process further. I have heard that merging the reads using vsearch followed by DADA2 denoise-single (single due to previously-merged reads using vsearch) will help to save a lot of sequence counts.
On the other hand, merging with DADA2 denoise-paired without going through vsearch will cause a huge loss of sequence reads.
Therefore, from this point onwards (after cutadapt), I am unsure if I should proceed with vsearch \> DADA2 denoise-single OR
just DADA2 denoise-paired.
Any suggestion will be much appreciated.
Thanks!
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### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [March 27, 2021, 8:22am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/2 "2021-03-27T08:22:47Z")
Hi!
I read about the same and tried both options with different datasets. Each time I got better results with Dada2 paired rather than with VSERCH - Dada2 single.
But maybe you should not trust my outputs and try both as well to make sure that you used best approach for your data
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### Author:  [@suetli19](https://forum.qiime2.org/u/suetli19)
#### Post date: [March 27, 2021, 8:39am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/3 "2021-03-27T08:39:59Z")
Hi @timanix ,
Thanks for the information!
When you said better results, which one are you referring to (like the sequence counts, etc. ?) Did you lost a lot of reads during the DADA2 step?
So, you performed Cutadapt first and then DADA2 paired to get you the better results that you mentioned, right?
Thank you!
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### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [March 27, 2021, 8:51am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/4 "2021-03-27T08:51:01Z")
> [@suetli19](#):
>
> When you said better results, which one are you referring to (like the sequence counts, etc. ?)
Yeah, I mean larger amount of output reads.
> [@suetli19](#):
>
> Did you lost a lot of reads during the DADA2 step?
I tried different trimming parameters in Dada2, and also tried to merge reads with VSEARCH and then denoise them in Deblur or DADA2 as single reads. With some trimming parameters I got less amount of output reads, with some - more. So it is important to try several parameters .
> [@suetli19](#):
>
> So, you performed Cutadapt first and then DADA2 paired to get you the better results that you mentioned, right?
Yeah, I got better results with Dada paired after cutadapt
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### Author:  [@ChrisKeefe](https://forum.qiime2.org/u/ChrisKeefe)
#### Post date: [March 29, 2021, 11:29pm UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/5 "2021-03-29T23:29:02Z")
According to the [DADA2 paper](https://www.nature.com/articles/nmeth.3869.epdf?author_access_token=hfTtC2mxuI5t44WUhsz05NRgN0jAjWel9jnR3ZoTv0N5gu3rLNk61gF4j2hXPcagLe964qdfd3GRw8OwyZxfEgsul8lwR1lEWykR3lWF30Dl_bZWMvTPwOdrwuiBUeYa),
> fastqFilter() implements filtering of fastq files that largely recapitulates the usearch fastq\_filter command (http:// [fastq\_filter command](http://www.drive5.com/usearch/manual/cmd_fastq_filter.html)). In short, this function trims sequences to a specified length, removes sequences shorter than that length, and filters based on the number of ambiguous bases, a minimum quality score, and the expected errors in a read. [18] fastqPairedFilter() implements the same trimming and filtering, but applies it to paired reads jointly, only outputting reads where both the forward and reverse reads pass the filter.
You're probably getting similar filtering behavior from vsearch and from DADA2, but `qiime dada2 denoise-paired` handles denoising and joining in one QIIME 2 command, and uses default behaviors that are internally consistent and "make sense" for high-quality ASVs.
I'm not an expert on DADA2, @suetli19, but I thought I'd throw in my two cents. "Join them separately and then have DADA2 pretend their single-end reads" feels a little hacky to me. I'm not aware of any reason it's a bad idea, I just don't like the semantics of it. Personally, I'd probably just go with DADA2, but as @timanix sagely suggested, you can always experiment with a couple approaches and see what works for your data.
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### Author:  [@ChrisKeefe](https://forum.qiime2.org/u/ChrisKeefe)
#### Post date: [March 29, 2021, 11:57pm UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/8 "2021-03-29T23:57:55Z")
Ok, I circled up with another mod on this, @suetli19, and this approach is a bad idea. 😆
Each base in your paired-end reads gets its own quality score from the sequencer. When a software tool joins two paired ends into one read, it needs to make a choice about what quality score to assign to the positions where the two reads overlap, so quality data gets lost.
As discussed in [this topic](https://forum.qiime2.org/t/can-dada2-be-carried-on-pre-joined-reads/7269/2), assigning new quality scores like this can mess with DADA 2's error model (which uses quality scores for denoising). Your results won't reflect the _actual_ quality scores assigned to the reads during sequencing, and may be less meaningful because of that.
Deblur doesn't care about quality scores. Feel free to experiment with pre-joining and denoising with deblur, but I'd recommend you avoid running pre-joined reads through DADA2.
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### Author:  [@suetli19](https://forum.qiime2.org/u/suetli19)
#### Post date: [March 30, 2021, 4:16am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/9 "2021-03-30T04:16:54Z")
Hi @ChrisKeefe ,
Your explanation is really clear and yeah, it does makes so much sense to me now. I'd probably just go with DADA2 denoise-paired since it's much better.
Thanks a lot!
Best,
Suet Li
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 30, 2021, 10:17am UTC](https://forum.qiime2.org/t/vsearch-and-dada2/19006/10 "2021-04-30T10:17:20Z")
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