# \#nanopore **URL:** https://forum.qiime2.org/tag/nanopore/166.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [NaMeco - pipeline for nanopore reads](https://forum.qiime2.org/t/nameco-pipeline-for-nanopore-reads/33864)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 1\ **Last updated:** [May 17, 2026, 9:25pm UTC](https://forum.qiime2.org/t/nameco-pipeline-for-nanopore-reads/33864 "2026-05-17T21:25:58Z")
Dear all, I am glad to share the pipeline for long nanopre 16S rRNA reads I was working on. The full description can be found on the GitHub page and in the paper. What it can do: So, NaMeco will preprocess the reads,… --- ## [help with PRONAME --clusterid fatal error](https://forum.qiime2.org/t/help-with-proname-clusterid-fatal-error/33513)
**Author:** [@ANTONIA\_NACIFF\_ROJAS](https://forum.qiime2.org/u/ANTONIA_NACIFF_ROJAS)\ **Replies:** 1\ **Last updated:** [July 29, 2025, 5:56pm UTC](https://forum.qiime2.org/t/help-with-proname-clusterid-fatal-error/33513 "2025-07-29T17:56:14Z")
I am trying to run the proname\_refine script from the PRONAME pipeline using the provided Singularity container. However, the process consistently fails with the error: Fatal error: Unrecognized string on command line (0… --- ## [Can I run QIIME2 on Multiplexed 16S ONT files?](https://forum.qiime2.org/t/can-i-run-qiime2-on-multiplexed-16s-ont-files/33263)
**Author:** [@Chenyu](https://forum.qiime2.org/u/Chenyu)\ **Replies:** 7\ **Last updated:** [July 8, 2025, 5:28pm UTC](https://forum.qiime2.org/t/can-i-run-qiime2-on-multiplexed-16s-ont-files/33263 "2025-07-08T17:28:38Z")
Hello all, I have a multiplexed .fastq file containing full-length 16S rRNA sequencing data generated by the MinION Mk1B platform. The structure of the file is shown below: I’m unsure whether QIIME2 can handle this … --- ## [Long read 16S amplicon Oxford Nanopore data](https://forum.qiime2.org/t/long-read-16s-amplicon-oxford-nanopore-data/32169)
**Author:** [@Shreya](https://forum.qiime2.org/u/Shreya)\ **Replies:** 2\ **Last updated:** [December 21, 2024, 1:57pm UTC](https://forum.qiime2.org/t/long-read-16s-amplicon-oxford-nanopore-data/32169 "2024-12-21T13:57:39Z")
Hello, I have recently got 16S v1-v9 full region ONT data from fecal samples (metagenomics). Can it be done by QIIME2 just like the short read sequencing analysis using DADA2 pipeline for generating ASVs? If no, then is … --- ## [Error when trying to align on OTUs](https://forum.qiime2.org/t/error-when-trying-to-align-on-otus/32045)
**Author:** [@sanduixxxe](https://forum.qiime2.org/u/sanduixxxe)\ **Replies:** 1\ **Last updated:** [December 4, 2024, 7:46pm UTC](https://forum.qiime2.org/t/error-when-trying-to-align-on-otus/32045 "2024-12-04T19:46:20Z")
I recently made a script to obtain Otu-table and phylogenetic tree, however in the sequence alignment step #4, it happens that a lot of time passes and it doesn't leave this part, however the CPU and RAM usage is close t… --- ## [nanopore sequences, some problems with](https://forum.qiime2.org/t/nanopore-sequences-some-problems-with/31994)
**Author:** [@sanduixxxe](https://forum.qiime2.org/u/sanduixxxe)\ **Replies:** 1\ **Last updated:** [November 27, 2024, 5:01pm UTC](https://forum.qiime2.org/t/nanopore-sequences-some-problems-with/31994 "2024-11-27T17:01:26Z")
I use nanopore promethion p2 solo. At the end of the sequencing, a folder is generated for each barcode, and to use qiime2 I make the manifest with the location of the .fastq files, but every time I try to run the follo… --- ## [Optimize DADA2 setup for Nanopore reads](https://forum.qiime2.org/t/optimize-dada2-setup-for-nanopore-reads/31928)
**Author:** [@zahir](https://forum.qiime2.org/u/zahir)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 6:24pm UTC](https://forum.qiime2.org/t/optimize-dada2-setup-for-nanopore-reads/31928 "2024-11-20T18:24:18Z")
Hello, This is my first time using qiime. I have full-length 16s metagenomics data sequence using MinION Mk1B. I have imported the single-end sequence to qiime: qiime tools import --type 'SampleData\[SequencesWithQu… --- ## [Workflow for/way to use qiime2 with nanopore data](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363)
**Author:** [@lmcfarland](https://forum.qiime2.org/u/lmcfarland)\ **Replies:** 5\ **Last updated:** [September 11, 2024, 8:55pm UTC](https://forum.qiime2.org/t/workflow-for-way-to-use-qiime2-with-nanopore-data/31363 "2024-09-11T20:55:44Z")
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… --- ## [Is there a way to use files from Nanopore in Qiime2 ?](https://forum.qiime2.org/t/is-there-a-way-to-use-files-from-nanopore-in-qiime2/25455)
**Author:** [@SingeunOh](https://forum.qiime2.org/u/SingeunOh)\ **Replies:** 5\ **Last updated:** [September 11, 2024, 12:54am UTC](https://forum.qiime2.org/t/is-there-a-way-to-use-files-from-nanopore-in-qiime2/25455 "2024-09-11T00:54:40Z")
Hello! I want to use files from Nanopore machine in Qiime2. I have looked through some questions and answers, but they have been quite a while. Hence, I want to ask similar topic at the moment. --------------My all prep… --- ## [MetONTIIME help](https://forum.qiime2.org/t/metontiime-help/30755)
**Author:** [@Mantella86](https://forum.qiime2.org/u/Mantella86)\ **Replies:** 6\ **Last updated:** [July 16, 2024, 10:53am UTC](https://forum.qiime2.org/t/metontiime-help/30755 "2024-07-16T10:53:32Z")
Hi everyone, does anyone have any step by step tutorials on how to use MetONTIIME. I will have nanopore data in the future and would like to use this but don't know where to start?. Best wishes --- ## [Importing Nanopore reads to QIIME2](https://forum.qiime2.org/t/importing-nanopore-reads-to-qiime2/29960)
**Author:** [@maysa1](https://forum.qiime2.org/u/maysa1)\ **Replies:** 5\ **Last updated:** [April 22, 2024, 6:19pm UTC](https://forum.qiime2.org/t/importing-nanopore-reads-to-qiime2/29960 "2024-04-22T18:19:43Z")
Hello all, I want to use QIIME 2 to analyse the nanopore reads I have for a total length of 16S. Since I already have V4 readings for the same samples and the analysis is available with epi2me, my goal is to gain higher… --- ## [16S full length nanopore to ASVs (new approach?)](https://forum.qiime2.org/t/16s-full-length-nanopore-to-asvs-new-approach/29968)
**Author:** [@LucasArg00](https://forum.qiime2.org/u/LucasArg00)\ **Replies:** 6\ **Last updated:** [April 18, 2024, 10:30pm UTC](https://forum.qiime2.org/t/16s-full-length-nanopore-to-asvs-new-approach/29968 "2024-04-18T22:30:41Z")
Hi everybody, I am new here and I have no better idea than to do something crazy. I have no idea if it is possible due to the fact of the sequencing nature. But could I map ASV reference sequences produced by QIIME2 into… --- ## [Error using MetONTIIME - Missing fromPath parameter](https://forum.qiime2.org/t/error-using-metontiime-missing-frompath-parameter/28345)
**Author:** [@Rebekah\_Henry1](https://forum.qiime2.org/u/Rebekah_Henry1)\ **Replies:** 2\ **Last updated:** [November 28, 2023, 11:06am UTC](https://forum.qiime2.org/t/error-using-metontiime-missing-frompath-parameter/28345 "2023-11-28T11:06:51Z")
Hi All, I have used QIIME2 alot but generally with Illumina data. I am not attempting to use MetONTIIME for nanopore through nextflow, but keep hitting the same error. Launching metontiime2.nf \[wise\_swartz\] DSL2 - revi… --- ## [Phylogenetic analysis of Nanopore 16S reads. How many subsampled reads will do?](https://forum.qiime2.org/t/phylogenetic-analysis-of-nanopore-16s-reads-how-many-subsampled-reads-will-do/23265)
**Author:** [@hoohugokim](https://forum.qiime2.org/u/hoohugokim)\ **Replies:** 7\ **Last updated:** [July 30, 2022, 10:57pm UTC](https://forum.qiime2.org/t/phylogenetic-analysis-of-nanopore-16s-reads-how-many-subsampled-reads-will-do/23265 "2022-07-30T22:57:46Z")
Hello! :person\_raising\_hand: It is my first time posting in the QIIME2 forum, which means my experience with QIIME2 has been only great so far without much ado. Recently I'm processing some Nanopore 16S V1–V9 reads and a… --- ## [can we process nanopore data using qiime2...?](https://forum.qiime2.org/t/can-we-process-nanopore-data-using-qiime2/16156)
**Author:** [@Anil\_Kumar\_Chauhan](https://forum.qiime2.org/u/Anil_Kumar_Chauhan)\ **Replies:** 5\ **Last updated:** [August 20, 2020, 7:31am UTC](https://forum.qiime2.org/t/can-we-process-nanopore-data-using-qiime2/16156 "2020-08-20T07:31:39Z")
can we process nanopore data using qiime2...? --- ## [q2ONT- q2 workflow for analysis of full length ONT 16S rRNA gene reads](https://forum.qiime2.org/t/q2ont-q2-workflow-for-analysis-of-full-length-ont-16s-rrna-gene-reads/12204)
**Author:** [@Deni\_Ribicic](https://forum.qiime2.org/u/Deni_Ribicic)\ **Replies:** 0\ **Last updated:** [October 29, 2019, 10:07am UTC](https://forum.qiime2.org/t/q2ont-q2-workflow-for-analysis-of-full-length-ont-16s-rrna-gene-reads/12204 "2019-10-29T10:07:31Z")
Dear qiimers, As it can be deduced from the title, I've generated a simple workflow to analyse full length 16S rRNA gene sequences coming from ONT platform. Hope to get some feedback from you, and open for suggestions … --- ## [16s Nanopore dada2 and deblur failed](https://forum.qiime2.org/t/16s-nanopore-dada2-and-deblur-failed/10614)
**Author:** [@ibrahim](https://forum.qiime2.org/u/ibrahim)\ **Replies:** 1\ **Last updated:** [July 10, 2019, 8:18pm UTC](https://forum.qiime2.org/t/16s-nanopore-dada2-and-deblur-failed/10614 "2019-07-10T20:18:45Z")
Hello, I have 16s rRNA reads from nanopore (1650 bp), i have cleaned and trimmed these fastq files with galaxy. When i try to use moving pictures tutorial i cannot pass the dada2 and deblur steps. I am using qiime2 201… --- ## [How to import Nanopore 16S data?](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215)
**Author:** [@HectorH](https://forum.qiime2.org/u/HectorH)\ **Replies:** 2\ **Last updated:** [July 31, 2018, 3:47pm UTC](https://forum.qiime2.org/t/how-to-import-nanopore-16s-data/5215 "2018-07-31T15:47:22Z")
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 questi… --- ## [Analysis of fastq files](https://forum.qiime2.org/t/analysis-of-fastq-files/3177)
**Author:** [@RENUKA](https://forum.qiime2.org/u/RENUKA)\ **Replies:** 5\ **Last updated:** [February 26, 2018, 7:13pm UTC](https://forum.qiime2.org/t/analysis-of-fastq-files/3177 "2018-02-26T19:13:03Z")
Hi I am new to qiime2. I have a fastq file generated from nanopore sequencing of around 42 MB. I want to analyse the sequences of that file. What programs can I use. The file is already with barcode.