# Workflow for/way to use qiime2 with nanopore data
**URL:** https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363
**Category:** Technical Support
**Tags:** taxonomy, nanopore, import
**Created:** [September 9, 2024, 4:48pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363 "2024-09-09T16:48:10Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@lmcfarland](https://forum.qiime2.org/u/lmcfarland)
#### Post date: [September 9, 2024, 4:48pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/1 "2024-09-09T16:48:10Z")
I've been using qiime for a while for research analyzing diet contents using eDNA (i.e., uncovering the taxonomy/species composition). Although I know qiime is meant for Illumina data, my data is nanopore sequences and I'm hoping others out there have used qiime with nanopore data too and can give me some guidance. The biggest issue I run into is that qiime filters sequences all to the same length but I need sequences to be different lengths. I have tried running vsearch outside of qiime to filter and cluster and then merged my data together and imported it back into qiime to run taxonomy analyses; However, I always run into issues, whether it be formatting or the code simply will just run forever without an output. Has anyone figured out a way to import multiple sequences of different lengths into qiime or have any suggestions for alternative pipelines/programs? I appreciate any feedback!
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [September 10, 2024, 5:48pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/2 "2024-09-10T17:48:22Z")
Helo Lauren,
Welcome to the forums! :qiime2:
So, the good news is that Qiime2 supports many input data types, including multiple sequencing types. Like, the Qiime2 DADA2 plugin supports Illumina, 'pyro' sequencing 454 and IonTorrent, and PacBio's CCS sequencing.
[https://docs.qiime2.org/2024.5/plugins/available/dada2/](https://docs.qiime2.org/2024.5/plugins/available/dada2/)
However, the underlying problem remains:
> [@lmcfarland](#):
>
> but I need sequences to be different lengths.
Variable length amplicons are not well supported, including on Illumina!
Did you use PCR to target an amplicon before NanoPore sequencing or was untargeted metagenome sequencing performed?
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### Author:  [@lmcfarland](https://forum.qiime2.org/u/lmcfarland)
#### Post date: [September 11, 2024, 4:55pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/3 "2024-09-11T16:55:17Z")
Hi, thanks for getting back to me!
Yes, I used PCR to target an amplicon before Nanopore sequencing. More specifically, I ran PCR with 5 different primer sets to target specific diet contents (i.e., plant, animal, fish, etc.,), and then all PCR products for a single sample were combined and taken through library preparation steps before being sequenced on a Nanopore device.
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [September 11, 2024, 5:27pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/4 "2024-09-11T17:27:06Z")
> [@lmcfarland](#):
>
> 5 different primer sets to target specific diet contents (
Okay, wow! That sounds a lot like this Ion Torrent kit, which is also multi-region.
> [@Possible Analysis Pipeline for Ion Torrent 16S Metagenomics Kit Data in QIIME2?](https://forum.qiime2.org/t/possible-analysis-pipeline-for-ion-torrent-16s-metagenomics-kit-data-in-qiime2/13476/):
>
> Hi QIIME2 community, My colleague @Lauren I have been using the Ion torrent 16S Metagenomics Kit to sequence some clinical samples that we have. Our sample sets are both longitudinal. The kit consists of two primer sets, one for V2-4-8 and one for V3-6,7-9. The products of the reactions are pooled per sample, and then the rest of library prep is completed. Each sample gets its own barcode. Ion Torrent produces single end reads. The issue here is that the reads from each of the 6 variable regio…
Multi-region kits have proven to be extraordinarily difficult.
Take a look at that thread and let us know what you want to try next.
There's another Lauren in that thread too, so maybe it's a curse! 👻
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### Author:  [@lmcfarland](https://forum.qiime2.org/u/lmcfarland)
#### Post date: [September 11, 2024, 8:17pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/5 "2024-09-11T20:17:36Z")
Great, thanks for your help! I'll check out that thread. I'm also going to try nanopores program and pipeline through epi2me that might work better for the varying sequence lengths, but we shall see!
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### Author:  [@devonorourke](https://forum.qiime2.org/u/devonorourke)
#### Post date: [September 11, 2024, 8:55pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/6 "2024-09-11T20:55:44Z")
Careful which EPI2ME workflow you use. Depends on your data type, but from what I can infer you want [wf-metagenomics](https://github.com/epi2me-labs/wf-metagenomics), not [wf-amplicon](https://github.com/epi2me-labs/wf-amplicon).
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [October 13, 2024, 9:22am UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363/8 "2024-10-13T09:22:48Z")
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