# NovaSeq data in QIIME2
**URL:** https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896
**Category:** User Support
**Created:** [September 27, 2021, 3:00pm UTC](https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896 "2021-09-27T15:00:45Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@AnkeWigger](https://forum.qiime2.org/u/AnkeWigger)
#### Post date: [September 27, 2021, 3:00pm UTC](https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896/1 "2021-09-27T15:00:45Z")
Hello,
I am new to bioinformatics and qiime2. For my research project I am doing a microbiome analysis in chickens. We want to send our samples to a sequencing company that uses novaseq6000. Although I have just learned how to import data into qiime2 (using the tutorials), I read the forum about complications of using novaseq data with qiime2 ([Consequences of using dada2 on NovaSeq data · Issue #791 · benjjneb/dada2 · GitHub](https://github.com/benjjneb/dada2/issues/791)).
I know my data will be delivered in FASTQ format, but I assume I will thus also get this problem when trying to perform the quality analysis.
Can anyone inform me how to import the NovaSeq data into QIIME2 so that I can perform a quality control before studying the microbiota composition?
Thank you in advance.
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [September 28, 2021, 4:26pm UTC](https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896/2 "2021-09-28T16:26:59Z")
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [September 28, 2021, 10:49pm UTC](https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896/3 "2021-09-28T22:49:40Z")
Hi @AnkeWigger,
Thanks for reaching out! Happy to provide some suggestions below:
> [@AnkeWigger](#):
>
> I have just learned how to import data into qiime2 (using the tutorials), I read the forum about complications of using novaseq data with qiime2 ([Consequences of using dada2 on NovaSeq data · Issue #791 · benjjneb/dada2 · GitHub](https://github.com/benjjneb/dada2/issues/791)).
>
> I know my data will be delivered in FASTQ format, but I assume I will thus also get this problem when trying to perform the quality analysis.
As discussed in [this forum post](https://forum.qiime2.org/t/has-anyone-looked-into-how-the-new-quality-binning-strategy-illumina-is-using-on-novaseq-sequencers-impacts-denoising-of-16s-data-what-are-the-best-practices/20859), you have a few options here:
- Use the dada2 R package with modifications as described by the Github link you shared above.
- Use the dada2 R package or q2-dada2 as it is, since there are several reports without any significant variations between using Dada2 as it is (R or Qiime2) and the modified version.
- Use Deblur which is not affected by changes in quality score binning.
Hopefully one of these options is a good solution for you!
Cheers :qiime2: 🦎
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [September 28, 2021, 10:49pm UTC](https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896/4 "2021-09-28T22:49:44Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [October 30, 2021, 4:50am UTC](https://forum.qiime2.org/t/novaseq-data-in-qiime2/20896/5 "2021-10-30T04:50:43Z")
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