# ITS2 and implementing cutadapt
**URL:** https://forum.qiime2.org/t/its2-and-implementing-cutadapt/1700
**Category:** Ideas and Suggestions
**Tags:** its
**Created:** [November 2, 2017, 4:07pm UTC](https://forum.qiime2.org/t/its2-and-implementing-cutadapt/1700 "2017-11-02T16:07:48Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@Baldribert](https://forum.qiime2.org/u/Baldribert)
#### Post date: [November 2, 2017, 4:07pm UTC](https://forum.qiime2.org/t/its2-and-implementing-cutadapt/1700/1 "2017-11-02T16:07:48Z")
Dear Qiime2 Team,
I have a question based on fungal ITS2 300bp paired-end MiSeq reads. Due to the variable region of ITS2, is it advisable to trim primer sequences using cutadapt (python-package) before merging your reads?
For a Miseq run paired-end 300bp, I understood, that you can end up sequencing into your reverse primer and vice-versa and that can influence your merging with DADA2. That would for example happen if you don't want to truncate the reads to achieve an overlap when you have a quality drop in the end of your R2 reads. Do you think implementing cutadapt into Qiime2 is therefore a good idea?
Cheers,
Robert
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [November 2, 2017, 10:25pm UTC](https://forum.qiime2.org/t/its2-and-implementing-cutadapt/1700/3 "2017-11-02T22:25:08Z")
Hi @Baldribert!
> [@Baldribert](#):
>
> is it advisable to trim primer sequences using cutadapt (python-package) before merging your reads
Yes --- there are a [few posts on the forum](https://forum.qiime2.org/search?q=cutadapt%20order%3Aviews) that touch on this, so I won't go into any details here. If you have more specific questions about this, feel free to open up a new thread under the [User Support](https://forum.qiime2.org/c/user-support) category!
> [@Baldribert](#):
>
> Do you think implementing cutadapt into Qiime2 is therefore a good idea?
A `q2-cutadapt` is currently on our radar, as one option in the [larger discussion](https://github.com/qiime2/q2-dada2/issues/32) of primer removal ✂ ✂ ✂! It would be really convenient if users were able to do this kind of thing within QIIME 2, and `cutadapt` certainly looks like a good candidate at the moment! Stay tuned! 📺
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [December 22, 2017, 5:55pm UTC](https://forum.qiime2.org/t/its2-and-implementing-cutadapt/1700/5 "2017-12-22T17:55:18Z")
[QIIME 2 2017.12](https://forum.qiime2.org/t/qiime-2-2017-12-release-is-now-live/2308) has a new `cutadapt` plugin!