Plugin like PEAR

Community Plugin Support
1

Hello, I need to merge my R1 and R2 fastq files before Cutadpt and DADA2. Are there any plugins in QIIME2 like PEAR, with several control parameters, like minimum size and maximum size, etc.

Thanks

2

Hi!

There is no PEAR plug in yet!
But you can use 'vsearch join pairs' for that:
https://docs.qiime2.org/2022.2/plugins/available/vsearch/join-pairs/

Or, you can use PEAR outside qiime2 and import the merged sequences.

In any case, for merged sequences you should not use DADA2, because the merging step alter the quality values (at least for the overlapping part) and this makes DADA2 assumptions on quality invalid.
You should use deblur instead.
Cheers and good luck
Luca

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3

Thanks a lot, seems join-pairs works perfectly for me.

4

Hi,
Just to add for completeness sake, there is actually a q2-pear plugin already (just not registered in the QIIME 2 library but I stumbled across this in a paper a while ago):

I have never used this and it is a few years old so I do not know if it is functional.

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5

Thanks a lot for letting me know.

6

Quick note: one of the authors and devs of PEAR, Tomáš Flouri, later on contributed to vsearch, and the vsearch joining algorithm uses an arguably better method for calculating post-joining Q-scores.

I wouldn't pair with PEAR, I would pair with vsearch!

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