# \#tutorial **URL:** https://forum.qiime2.org/tag/tutorial/40.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Using RESCRIPt's 'extract-seq-segments' to extract reference sequences without PCR primer pairs.](https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 5\ **Last updated:** [November 14, 2023, 7:22pm UTC](https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618 "2023-11-14T19:22:00Z")
:construction: Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. Please feel free to ask questions and provide feedback. Happy :qiime2:ing! … --- ## [Train a taxonomy classifier by extracting an amplicon region from a curated sequence alignment (using SILVA as an example).](https://forum.qiime2.org/t/train-a-taxonomy-classifier-by-extracting-an-amplicon-region-from-a-curated-sequence-alignment-using-silva-as-an-example/34289)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 0\ **Last updated:** [August 12, 2026, 5:46pm UTC](https://forum.qiime2.org/t/train-a-taxonomy-classifier-by-extracting-an-amplicon-region-from-a-curated-sequence-alignment-using-silva-as-an-example/34289 "2026-08-12T17:46:15Z")
:construction: Please consider this tutorial a living document , which may change based upon community feedback and ongoing plugin development. :construction: Overview: There are several approaches within QIIME 2, and… --- ## [Python Tutorial: Data Visualization with Dokdo API](https://forum.qiime2.org/t/python-tutorial-data-visualization-with-dokdo-api/17380)
**Author:** [@sbslee](https://forum.qiime2.org/u/sbslee)\ **Replies:** 51\ **Last updated:** [September 18, 2025, 7:57pm UTC](https://forum.qiime2.org/t/python-tutorial-data-visualization-with-dokdo-api/17380 "2025-09-18T19:57:16Z")
This tutorial has gotten so big that apparently the text body exceeded the maximum number of characters one can enter in a post (99,000)! Therefore, I will leave a link to Dokdo API for those who are interested in seeing… --- ## [q2-fondue: sra-tools configuration](https://forum.qiime2.org/t/q2-fondue-sra-tools-configuration/33360)
**Author:** [@yangyue](https://forum.qiime2.org/u/yangyue)\ **Replies:** 8\ **Last updated:** [July 2, 2025, 1:02pm UTC](https://forum.qiime2.org/t/q2-fondue-sra-tools-configuration/33360 "2025-07-02T13:02:55Z")
I've download all of the run IDs of the dataset of the moshpit tutorial, using the default code with my e-mail address, but only changed the code with "--p-threads 11", but every run ID need to experience seven times of … --- ## [step by step tutorial specifically for qiime2-amplicon-2024.10](https://forum.qiime2.org/t/step-by-step-tutorial-specifically-for-qiime2-amplicon-2024-10/32484)
**Author:** [@EugeniaSH](https://forum.qiime2.org/u/EugeniaSH)\ **Replies:** 6\ **Last updated:** [February 12, 2025, 7:49pm UTC](https://forum.qiime2.org/t/step-by-step-tutorial-specifically-for-qiime2-amplicon-2024-10/32484 "2025-02-12T19:49:58Z")
Thank you for the step bu step tutorial. I am very new in Qiime2, and starting to migrate to the amplicon mode. I am not sure if I should do all the steps of the testing with greengenes, or stop after dereplicating af… --- ## [How to train a GTDB SSU classifier using RESCRIPt](https://forum.qiime2.org/t/how-to-train-a-gtdb-ssu-classifier-using-rescript/25725)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 2\ **Last updated:** [July 23, 2024, 3:53pm UTC](https://forum.qiime2.org/t/how-to-train-a-gtdb-ssu-classifier-using-rescript/25725 "2024-07-23T15:53:56Z")
:construction: Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. Please feel free to ask questions and provide feedback. Happy :qiime2:ing! H… --- ## [Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences](https://forum.qiime2.org/t/q2-itsxpress-a-tutorial-on-a-qiime-2-plugin-to-trim-its-sequences/5780)
**Author:** [@Adam\_Rivers](https://forum.qiime2.org/u/Adam_Rivers)\ **Replies:** 24\ **Last updated:** [January 10, 2025, 2:58am UTC](https://forum.qiime2.org/t/q2-itsxpress-a-tutorial-on-a-qiime-2-plugin-to-trim-its-sequences/5780 "2025-01-10T02:58:23Z")
ITSxpress: a QIIME 2 plugin to trim ITS sequences Adam R. Rivers - USDA Agricultural Research Service Sveinn V. Einarsson - Dep. Microbiology and Cell Science, U. Florida & USDA Agricultural Research Service Background … --- ## [How to train a UNITE classifier using RESCRIPt](https://forum.qiime2.org/t/how-to-train-a-unite-classifier-using-rescript/28285)
**Author:** [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Replies:** 8\ **Last updated:** [January 3, 2025, 2:37pm UTC](https://forum.qiime2.org/t/how-to-train-a-unite-classifier-using-rescript/28285 "2025-01-03T14:37:03Z")
:construction: This tutorial is a work in progress. Please leave us questions and comments so we can better help you use this database. All feedback is welcome. If you are looking for a pre-trained ITS classifier, you c… --- ## [NovaSeq and Dada2 incompatibility.](https://forum.qiime2.org/t/novaseq-and-dada2-incompatibility/25865)
**Author:** [@Johanndb](https://forum.qiime2.org/u/Johanndb)\ **Replies:** 10\ **Last updated:** [August 6, 2024, 3:21pm UTC](https://forum.qiime2.org/t/novaseq-and-dada2-incompatibility/25865 "2024-08-06T15:21:50Z")
Dear All, I have been analysing NovaSeq 6000 16s rRNA V4-V5 data for the past few months. This is my first experience with NGS data analysis. As a novice, I was sideswiped by the fact that NovaSeq results were very diff… --- ## [Automatic Manifest Maker in Python3](https://forum.qiime2.org/t/automatic-manifest-maker-in-python3/8595)
**Author:** [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)\ **Replies:** 3\ **Last updated:** [January 26, 2024, 6:00pm UTC](https://forum.qiime2.org/t/automatic-manifest-maker-in-python3/8595 "2024-01-26T18:00:23Z")
Hello all! Since joining this community my coding skill has improved quite a lot. When I first started I made this tutorial here, which is functional, but not ideal. I decided to update it to be a bit more useful for pe… --- ## [q2-gcn-norm: plugin for normalizing sequences by 16S rRNA gene copy number](https://forum.qiime2.org/t/q2-gcn-norm-plugin-for-normalizing-sequences-by-16s-rrna-gene-copy-number/12715)
**Author:** [@jwchen](https://forum.qiime2.org/u/jwchen)\ **Replies:** 11\ **Last updated:** [October 11, 2023, 11:09pm UTC](https://forum.qiime2.org/t/q2-gcn-norm-plugin-for-normalizing-sequences-by-16s-rrna-gene-copy-number/12715 "2023-10-11T23:09:32Z")
Thanks to the detailed developer documentation, the plugin finally comes out :partying\_face: If you find bugs or have suggestions, please make a post on this forum and on the Github repository. q2-gcn-norm QIIME 2 plug… --- ## [454 data: errors right up front! Qiime tools import errors](https://forum.qiime2.org/t/454-data-errors-right-up-front-qiime-tools-import-errors/27066)
**Author:** [@jvoelschow](https://forum.qiime2.org/u/jvoelschow)\ **Replies:** 7\ **Last updated:** [July 17, 2023, 6:08pm UTC](https://forum.qiime2.org/t/454-data-errors-right-up-front-qiime-tools-import-errors/27066 "2023-07-17T18:08:52Z")
Hi there, I'm pretty new to QIIME2, so this is probably something super simple. I'm using v2023.5 and trying to run thru the 454 tutorial, as I have old but import data I need to analyze, however I'm running into an er… --- ## [Demultiplexing and Trimming Adapters from Reads with q2-cutadapt](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313)
**Author:** [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Replies:** 4\ **Last updated:** [March 12, 2020, 9:52pm UTC](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313 "2020-03-12T21:52:41Z")
:exclamation: :exclamation: :exclamation: NOTE :exclamation: :exclamation: :exclamation: This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available… --- ## [Alpha and Beta Diversity Explanations and Commands](https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 6\ **Last updated:** [September 15, 2018, 5:06pm UTC](https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282 "2018-09-15T17:06:14Z")
About the Alpha and Beta Diversity Analysis Tutorial This Alpha and Beta Diversity Community Tutorial (run using QIIME 2017.12) walks you through analyzing the alpha and beta diversity of a sample dataset. Below you will… --- ## [Atacama tutorial](https://forum.qiime2.org/t/atacama-tutorial/25534)
**Author:** [@Oleg](https://forum.qiime2.org/u/Oleg)\ **Replies:** 1\ **Last updated:** [March 7, 2023, 5:13pm UTC](https://forum.qiime2.org/t/atacama-tutorial/25534 "2023-03-07T17:13:29Z")
Hello! I was wondering if someone knows where to find the description of metadata in Atacama tutorial? I read the original paper, and but they do not mention some of the features, for example, I was wondering what's th… --- ## [Visualizing 'omic feature rankings and log-ratios with q2-qurro](https://forum.qiime2.org/t/visualizing-omic-feature-rankings-and-log-ratios-with-q2-qurro/14795)
**Author:** [@fedarko](https://forum.qiime2.org/u/fedarko)\ **Replies:** 0\ **Last updated:** [May 5, 2020, 11:46pm UTC](https://forum.qiime2.org/t/visualizing-omic-feature-rankings-and-log-ratios-with-q2-qurro/14795 "2020-05-05T23:46:22Z")
Visualizing 'omic feature rankings and log-ratios with q2-qurro Hi everyone! We recently put together a new visualization tool that can be used through QIIME 2 named Qurro. A paper was just published on the tool last wee… --- ## [Tutorial: Basic Command Line Interface for Beginners to Qiime2](https://forum.qiime2.org/t/tutorial-basic-command-line-interface-for-beginners-to-qiime2/6804)
**Author:** [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)\ **Replies:** 3\ **Last updated:** [November 16, 2020, 10:08am UTC](https://forum.qiime2.org/t/tutorial-basic-command-line-interface-for-beginners-to-qiime2/6804 "2020-11-16T10:08:02Z")
Hello all, it came up here, that it might be useful to have a tutorial for basic CLI (command line interface) commands, to link to for when people are struggling using an unfamiliar environment. If anyone has any amendme… --- ## [Facing problem while importing single end sequences](https://forum.qiime2.org/t/facing-problem-while-importing-single-end-sequences/22201)
**Author:** [@Rishikesh12](https://forum.qiime2.org/u/Rishikesh12)\ **Replies:** 2\ **Last updated:** [February 23, 2022, 9:02am UTC](https://forum.qiime2.org/t/facing-problem-while-importing-single-end-sequences/22201 "2022-02-23T09:02:09Z")
I have 24 samples in the fastq.gz format. all reads are single end and i want to import those data into qiime2 but it throwing some errors. I don't have barcode sequences data. Can i proceed without barcode sequences or … --- ## [Denoising and Clustering from Tutorials](https://forum.qiime2.org/t/denoising-and-clustering-from-tutorials/21941)
**Author:** [@Jhlee](https://forum.qiime2.org/u/Jhlee)\ **Replies:** 1\ **Last updated:** [January 21, 2022, 3:09pm UTC](https://forum.qiime2.org/t/denoising-and-clustering-from-tutorials/21941 "2022-01-21T15:09:21Z")
Hi. Tutorial says Denoising and clustering Congratulations on getting this far! Denoising and clustering steps are slightly less confusing than importing and demultiplexing! The names for these steps are very descripti… --- ## [Tutorial "Moving pictures" | alpha rarefaction | the question about right palm jumping](https://forum.qiime2.org/t/tutorial-moving-pictures-alpha-rarefaction-the-question-about-right-palm-jumping/21464)
**Author:** [@JeremyTournayre](https://forum.qiime2.org/u/JeremyTournayre)\ **Replies:** 5\ **Last updated:** [December 11, 2021, 12:48am UTC](https://forum.qiime2.org/t/tutorial-moving-pictures-alpha-rarefaction-the-question-about-right-palm-jumping/21464 "2021-12-11T00:48:56Z")
Hello, I'm wondering what is the correct answer for this "Question" in the moving pictures tutorial: When grouping samples by “body-site” and viewing the alpha rarefaction plot for the “observed\_features” metric, the … --- ## [q2-srs: QIIME2 plugin for library size normalization by scaling with ranked subsampling (SRS)](https://forum.qiime2.org/t/q2-srs-qiime2-plugin-for-library-size-normalization-by-scaling-with-ranked-subsampling-srs/17661)
**Author:** [@vheidrich](https://forum.qiime2.org/u/vheidrich)\ **Replies:** 3\ **Last updated:** [December 6, 2021, 8:14pm UTC](https://forum.qiime2.org/t/q2-srs-qiime2-plugin-for-library-size-normalization-by-scaling-with-ranked-subsampling-srs/17661 "2021-12-06T20:14:11Z")
Hi everyone, I am happy to announce that the SRS QIIME 2 plugin is out! SRS is an alternative library size normalization tool. For details, take a look at the SRS paper or go to the @lukasbeule's topic on how SRS works… --- ## [QIIME 2 plugin for ZSH](https://forum.qiime2.org/t/qiime-2-plugin-for-zsh/19865)
**Author:** [@misialq](https://forum.qiime2.org/u/misialq)\ **Replies:** 0\ **Last updated:** [June 11, 2021, 10:15am UTC](https://forum.qiime2.org/t/qiime-2-plugin-for-zsh/19865 "2021-06-11T10:15:11Z")
After having installed, uninstalled and reinstalled a number of Q2 environments I figured there was room for making that repetitive process slightly easier. As zsh is these days one of the most popular shells, I wrapped … --- ## [Transferring Qiita Artifacts to Qiime2](https://forum.qiime2.org/t/transferring-qiita-artifacts-to-qiime2/4790)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 0\ **Last updated:** [June 28, 2018, 10:23pm UTC](https://forum.qiime2.org/t/transferring-qiita-artifacts-to-qiime2/4790 "2018-06-28T22:23:31Z")
About the Transferring Qiita Artifacts to Qiime2 Tutorial This Transferring Qiita Artifacts to Qiime2 Community Tutorial (run using QIIME 2018.6) walks you through converting your data from Qiita to .qza files so you can… --- ## [Why are my beta diversity results different from the tutorial?](https://forum.qiime2.org/t/why-are-my-beta-diversity-results-different-from-the-tutorial/15676)
**Author:** [@anirban.mcgill](https://forum.qiime2.org/u/anirban.mcgill)\ **Replies:** 5\ **Last updated:** [July 9, 2020, 3:30pm UTC](https://forum.qiime2.org/t/why-are-my-beta-diversity-results-different-from-the-tutorial/15676 "2020-07-09T15:30:40Z")
Hi Dr. Debelius @jwdebelius You answered my queries-thanks a lot! Also, putting multiple columns on the metadata for both numeric and categorical is a clever hack-thanks! There's one other thing that's been bugging me … --- ## [Normalize ASV by 16S copy number](https://forum.qiime2.org/t/normalize-asv-by-16s-copy-number/12624)
**Author:** [@jwchen](https://forum.qiime2.org/u/jwchen)\ **Replies:** 3\ **Last updated:** [November 27, 2019, 7:08pm UTC](https://forum.qiime2.org/t/normalize-asv-by-16s-copy-number/12624 "2019-11-27T19:08:14Z")
Hi all, I recently wrote a python script that can normalize ASVs with 16S rRNA gene copy number. Hope it works well and suggestions are welcome! Introduction: Normalize sequences by 16S rRNA gene copy number (GCN) base… --- ## [The solution about the MemoryError when training classifier with SILVA 132](https://forum.qiime2.org/t/the-solution-about-the-memoryerror-when-training-classifier-with-silva-132/13668)
**Author:** [@Daryl](https://forum.qiime2.org/u/Daryl)\ **Replies:** 2\ **Last updated:** [February 24, 2020, 1:57pm UTC](https://forum.qiime2.org/t/the-solution-about-the-memoryerror-when-training-classifier-with-silva-132/13668 "2020-02-24T13:57:47Z")
hello~ A few days ago, I used the silver 99%132 database to train my classifier by qiime feature-classifier fit-classifier-naive-bayes . Unfortunately, I had the same problems about MemoryError as everyone else. There … --- ## [Q2-phylogeny: Community Tutorial](https://forum.qiime2.org/t/q2-phylogeny-community-tutorial/4455)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 0\ **Last updated:** [June 5, 2018, 11:44pm UTC](https://forum.qiime2.org/t/q2-phylogeny-community-tutorial/4455 "2018-06-05T23:44:57Z")
This community tutorial has been migrated to our official documentation. Please refer to that tutorial instead. ▶ Click to see original community tutorial --- ## [Automatic Manifest Maker in R](https://forum.qiime2.org/t/automatic-manifest-maker-in-r/2921)
**Author:** [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)\ **Replies:** 4\ **Last updated:** [September 4, 2019, 12:48am UTC](https://forum.qiime2.org/t/automatic-manifest-maker-in-r/2921 "2019-09-04T00:48:02Z")
Here I present my tutorial for making a 'Manifest.csv' automatically using an R conda environment, to be used to import data according to the " “Fastq manifest” formats" part of the Importing data tutorial. I wrote this… --- ## [LEfSE after Qiime2 new problem](https://forum.qiime2.org/t/lefse-after-qiime2-new-problem/10108)
**Author:** [@fdm](https://forum.qiime2.org/u/fdm)\ **Replies:** 11\ **Last updated:** [June 12, 2019, 11:37am UTC](https://forum.qiime2.org/t/lefse-after-qiime2-new-problem/10108 "2019-06-12T11:37:29Z")
Dear All, I am newby to Qiime2, but with firum supprt I have solved a series of probem. Thank in advance. But I have a trouble with the LEfSE analysis. Briefly, I have follwed the indication of the Dr Bemjamin obtaini… --- ## [How to import paired-end fastq files](https://forum.qiime2.org/t/how-to-import-paired-end-fastq-files/8058)
**Author:** [@nbourre](https://forum.qiime2.org/u/nbourre)\ **Replies:** 17\ **Last updated:** [April 4, 2019, 4:38pm UTC](https://forum.qiime2.org/t/how-to-import-paired-end-fastq-files/8058 "2019-04-04T16:38:58Z")
Hey guys, I'm totally new to bioinformatics. I have a degree in computer science and very basic knowledge in biology. I have been mandated to start to learn QIIME2 for a project. So I started the "Moving pictures" tutor… [Next page](https://forum.qiime2.org/tag/tutorial/40.md?match_all_tags=true&page=1&tags%5B%5D=tutorial)