# PacBio hifi reads data analysis through qimme2
**URL:** https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726
**Category:** User Support
**Created:** [July 27, 2022, 7:02pm UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726 "2022-07-27T19:02:03Z")
**Posts on this page:** 8
**Page:** 1
### Author:  [@rr220](https://forum.qiime2.org/u/rr220)
#### Post date: [July 27, 2022, 7:02pm UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/1 "2022-07-27T19:02:03Z")
Hi,
I wanted to know can we use the QIIME2 pipeline to runPacBio hifi reads data. I have received the data files in following format: demultiplex.bc1005--bc1033.hifi\_reads.fastq.gz
Where can I find the command line to run this project using QIIME2 (via Terminal Mac). I did look at [denoise-ccs: Denoise and dereplicate single-end Pacbio CCS — QIIME 2 2022.2.0 documentation](https://docs.qiime2.org/2022.2/plugins/available/dada2/denoise-ccs/) but unable to locate tutorial and command line.
Best,
R
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [July 28, 2022, 7:34pm UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/2 "2022-07-28T19:34:27Z")
Hi @rr220,
Thanks for reaching out!
We don't have a designated tutorial for this specific method, but the documentation that you linked is exactly what I'd recommend reading over in order to better understand how this method works. It has details on the input type, required parameters, and what your expected output should be.
I would give that another look over, and let us know if you have any specific questions regarding running that or any issues you run into along the way!
Cheers 🦎
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### Author:  [@rr220](https://forum.qiime2.org/u/rr220)
#### Post date: [July 29, 2022, 12:39am UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/3 "2022-07-29T00:39:41Z")
Hi,
Thank you so much for your response. I have following questions:
1. Is this integrated with QIIME2? or can only be done in R?
2. Can I use regular QIIME2 pipeline with PacBio for get diversity output?
Thank you so much!
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### Author:  [@rr220](https://forum.qiime2.org/u/rr220)
#### Post date: [July 29, 2022, 2:46pm UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/4 "2022-07-29T14:46:13Z")
I have one more query: I found this link which mentions QIMME2 can be used for Pacbio reads. Is this information accurate.
[https://github-wiki-see.page/m/PacificBiosciences/pb-16S-nf/wiki/Analyzing-PacBio-HiFi-Mock-Community-16S-Data-with-QIIME-2](https://github-wiki-see.page/m/PacificBiosciences/pb-16S-nf/wiki/Analyzing-PacBio-HiFi-Mock-Community-16S-Data-with-QIIME-2)
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [August 1, 2022, 2:24am UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/5 "2022-08-01T02:24:35Z")
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [August 1, 2022, 6:57pm UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/6 "2022-08-01T18:57:35Z")
Hi @rr220,
> [@rr220](#):
>
> Is this integrated with QIIME2? or can only be done in R?
The [original link that you provided](https://docs.qiime2.org/2022.2/plugins/available/dada2/denoise-ccs/) is from our documentation - what this means is that the command `qiime denoise-ccs` is available for use within the QIIME 2 Framework. So as long as you have QIIME 2 installed on your machine, you will be able to utilize this command on single end Pacbio CCS reads.
> [@rr220](#):
>
> Can I use regular QIIME2 pipeline with PacBio for get diversity output?
Yes - from the documentation linked above, you'll see that the input type for `qiime denoise-ccs` is single-end demultiplexed PacBio CCS sequences, and the output types will be as follows:
```auto
--o-table ARTIFACT FeatureTable[Frequency]
The resulting feature table.
--o-representative-sequences ARTIFACT FeatureData[Sequence]
The resulting feature sequences. Each feature in the
feature table will be represented by exactly one
sequence.
--o-denoising-stats ARTIFACT SampleData[DADA2Stats]
```
Hopefully this helps provide some clarification - let us know if you have any additional questions!
Cheers 🦎
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [August 1, 2022, 6:57pm UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/7 "2022-08-01T18:57:39Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 2, 2022, 12:58am UTC](https://forum.qiime2.org/t/pacbio-hifi-reads-data-analysis-through-qimme2/23726/8 "2022-09-02T00:58:07Z")
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