# How to import Nanopore 16S data?

**URL:** https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215
**Category:** User Support
**Tags:** nanopore, import
**Created:** [July 24, 2018, 11:49am UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215 "2018-07-24T11:49:08Z")
**Posts on this page:** 6
**Page:** 1

<div class="post-metadata">

### Author: ![HectorH](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/bbe5ce/32.png) [@HectorH](https://forum.qiime2.org/u/HectorH)
#### Post date: [July 24, 2018, 11:49am UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215/1 "2018-07-24T11:49:08Z")

</div>

Hi there,  
I have single-end 16S sequencing data obtained with a MinION (SQK-RAB204) that I'd like to analyze with Qiime2.  
I used Albacore for basecalling and demultiplexed into 6 independent fastq files. Similar questions have been asked some time ago, but I couldn't find a clear pipeline.  
For the first step: what is the best way to import this type of data to Qiime2? can I use, for example, "Casava 1.8 single-end demultiplexed fastq"?.  
Thanks a lot!

---

<div class="post-metadata">

### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [July 24, 2018, 12:48pm UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215/2 "2018-07-24T12:48:34Z")

</div>



---

<div class="post-metadata">

### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [July 30, 2018, 2:06pm UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215/3 "2018-07-30T14:06:13Z")

</div>

Hi @HectorH,

Sorry for the very delayed response.

I don't think we have a lot of experience with MinION, but, I think your idea of using the Casava 1.8 format should work fine. You can also give the [fastq manifest](https://docs.qiime2.org/2018.6/tutorials/importing/#fastq-manifest-formats) a shot.

Out of curiousity, what does MinION data look like? It would be cool to be able to support this more directly in QIIME 2.

---

<div class="post-metadata">

### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [July 30, 2018, 2:06pm UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215/4 "2018-07-30T14:06:15Z")

</div>



---

<div class="post-metadata">

### Author: ![HectorH](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/bbe5ce/32.png) [@HectorH](https://forum.qiime2.org/u/HectorH)
#### Post date: [July 31, 2018, 3:47pm UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215/5 "2018-07-31T15:47:22Z")

</div>

thank you @ebolyen ,  
I managed to import my data using the manifest:

> qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path se\_33\_manifest --output-path single-end-demux.qza --source-format SingleEndFastqManifestPhred33

so probably there is no need to try the Casava format.  
I will test now different options for trimming and feature table construction (my reads are about 1.5 kb).  
Thanks!

---

<div class="post-metadata">

### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 31, 2018, 9:47pm UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215/6 "2018-08-31T21:47:25Z")

</div>

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.