# \#taxonomy **URL:** https://forum.qiime2.org/tag/taxonomy/29.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Reformat OTU table for use in FUNGuild](https://forum.qiime2.org/t/reformat-otu-table-for-use-in-funguild/33861)
**Author:** [@mhog](https://forum.qiime2.org/u/mhog)\ **Replies:** 2\ **Last updated:** [September 28, 2026, 6:24am UTC](https://forum.qiime2.org/t/reformat-otu-table-for-use-in-funguild/33861 "2026-09-28T06:24:35Z")
Hey guys, I hope I’ve put this in the right category! I’m trying to assign my fungal ITS taxa functional guilds with FUNGuild, but to do so I need an OTU able formatted a specific way. I’ve managed to use ITSxpress to e… --- ## [16S Sequencing for Species-Level Resolution](https://forum.qiime2.org/t/16s-sequencing-for-species-level-resolution/34284)
**Author:** [@Jeremie\_Auger](https://forum.qiime2.org/u/Jeremie_Auger)\ **Replies:** 5\ **Last updated:** [September 8, 2026, 12:59pm UTC](https://forum.qiime2.org/t/16s-sequencing-for-species-level-resolution/34284 "2026-09-08T12:59:15Z")
Hi qiime2 community. (This post is long, but needs some context.) The short story is that I think that the qiime2 classification (or taxa collapse) step are stopping species-level classification for vaginal swab microbi… --- ## [Bug in new SILVA 144 taxmap file](https://forum.qiime2.org/t/bug-in-new-silva-144-taxmap-file/34308)
**Author:** [@hdeel](https://forum.qiime2.org/u/hdeel)\ **Replies:** 6\ **Last updated:** [September 3, 2026, 2:48pm UTC](https://forum.qiime2.org/t/bug-in-new-silva-144-taxmap-file/34308 "2026-09-03T14:48:51Z")
Hello Q2 folks, I was unable to find this reported on the forum anywhere, so I thought it would be good to make a quick post. I am working on creating a custom taxonomic classifier with the new SILVA 144 version (follow… --- ## [pre-trained UNITE ITS classifiers for QIIME 2026.7 and scikit-learn=1.7.1](https://forum.qiime2.org/t/pre-trained-unite-its-classifiers-for-qiime-2026-7-and-scikit-learn-1-7-1/24140)
**Author:** [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Replies:** 15\ **Last updated:** [August 31, 2026, 6:59pm UTC](https://forum.qiime2.org/t/pre-trained-unite-its-classifiers-for-qiime-2026-7-and-scikit-learn-1-7-1/24140 "2026-08-31T18:59:19Z")
UNITE version 10.0 was updated on 2025-02-19, and I've built classifiers for it compatible with the newest version of Qiime2: New in 2026 Updated to qiime2-amplicon-2026.7 that includes scikit-learn=1.7.1 I've rewrit… --- ## [extract-seq-segments: number of reads vs accuracy of reads.](https://forum.qiime2.org/t/extract-seq-segments-number-of-reads-vs-accuracy-of-reads/34293)
**Author:** [@deClare125](https://forum.qiime2.org/u/deClare125)\ **Replies:** 3\ **Last updated:** [August 19, 2026, 7:06pm UTC](https://forum.qiime2.org/t/extract-seq-segments-number-of-reads-vs-accuracy-of-reads/34293 "2026-08-19T19:06:13Z")
Hi Mike, I read this from your post: "But if you are hoping to strictly stay within the bounds of your expected amplicon length, then Id simply do more iterations, at a much higher similarity, say 90% then go up.", and … --- ## [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… --- ## [RESCRIPt-evaluate](https://forum.qiime2.org/t/rescript-evaluate/34265)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 0\ **Last updated:** [July 27, 2026, 7:34pm UTC](https://forum.qiime2.org/t/rescript-evaluate/34265 "2026-07-27T19:34:46Z")
RESCRIPt-evaluate History: Due to dependency conflicts with other branches of rachis (i.e. moshpit & pathogenome), the actions evaluate-cross-validate and evaluate-fit-classifier were removed from recent versions of RESC… --- ## [Naive Bayes classifier trained on a custom NCBI RefSeq V3-V4 database classifies almost all ASVs as same species](https://forum.qiime2.org/t/naive-bayes-classifier-trained-on-a-custom-ncbi-refseq-v3-v4-database-classifies-almost-all-asvs-as-same-species/34249)
**Author:** [@Kris\_P](https://forum.qiime2.org/u/Kris_P)\ **Replies:** 1\ **Last updated:** [July 15, 2026, 3:00pm UTC](https://forum.qiime2.org/t/naive-bayes-classifier-trained-on-a-custom-ncbi-refseq-v3-v4-database-classifies-almost-all-asvs-as-same-species/34249 "2026-07-15T15:00:35Z")
Hello, I am currently using QIIME 2 2026.1. Previously, I built a custom full-length NCBI RefSeq 16S classifier using rescript get-ncbi-data with BioProject 33175 (Bacteria). I first created this workflow in 2023 and ha… --- ## [DeepTaxa, a QIIME 2 plugin for 16S taxonomy](https://forum.qiime2.org/t/deeptaxa-a-qiime-2-plugin-for-16s-taxonomy/34228)
**Author:** [@ahmedmoustafa](https://forum.qiime2.org/u/ahmedmoustafa)\ **Replies:** 1\ **Last updated:** [July 2, 2026, 10:46am UTC](https://forum.qiime2.org/t/deeptaxa-a-qiime-2-plugin-for-16s-taxonomy/34228 "2026-07-02T10:46:59Z")
Hi everyone, I want to share a QIIME 2 plugin that we just released for DeepTaxa. Maybe it is useful for your 16S analysis. DeepTaxa is a deep learning model for the taxonomy of 16S rRNA sequences. It predicts all seve… --- ## [ITS Classifier: Extract reference reads - HiSeq:](https://forum.qiime2.org/t/its-classifier-extract-reference-reads-hiseq/34164)
**Author:** [@fabipc](https://forum.qiime2.org/u/fabipc)\ **Replies:** 2\ **Last updated:** [May 31, 2026, 6:42am UTC](https://forum.qiime2.org/t/its-classifier-extract-reference-reads-hiseq/34164 "2026-05-31T06:42:14Z")
Hello, I have a quick question. Our lab decided to try and use HISeq to test if we get similar or better resolution (taxonomic resolution), for our samples as we do with ASVs.However, the DADA2 parameters that give me t… --- ## [Merging NGS with TGS?](https://forum.qiime2.org/t/merging-ngs-with-tgs/34179)
**Author:** [@Patrick\_Wu](https://forum.qiime2.org/u/Patrick_Wu)\ **Replies:** 3\ **Last updated:** [May 20, 2026, 6:21am UTC](https://forum.qiime2.org/t/merging-ngs-with-tgs/34179 "2026-05-20T06:21:03Z")
As the title suggests, one of the clients at my core lab is asking me to analyze a batch of data generated by NGS with a new batch of data generated by TGS. Now I have done DADA2 -\> merge for two different NGS runs using… --- ## [Data analysis from Oxford Nanopore](https://forum.qiime2.org/t/data-analysis-from-oxford-nanopore/34180)
**Author:** [@EMI012](https://forum.qiime2.org/u/EMI012)\ **Replies:** 1\ **Last updated:** [May 19, 2026, 2:35pm UTC](https://forum.qiime2.org/t/data-analysis-from-oxford-nanopore/34180 "2026-05-19T14:35:52Z")
Hello, I am analyzing Nanopore 16S data (24 samples), but my reads are much shorter than expected (300–500 bp instead of ~1500 bp). What is the best QIIME2 approach in this case? Should I use DADA2 or switch to OTU c… --- ## [ITS2 classification: identical sequences but different results (DADA2 vs merged)](https://forum.qiime2.org/t/its2-classification-identical-sequences-but-different-results-dada2-vs-merged/34107)
**Author:** [@sissiyun](https://forum.qiime2.org/u/sissiyun)\ **Replies:** 6\ **Last updated:** [April 7, 2026, 6:38am UTC](https://forum.qiime2.org/t/its2-classification-identical-sequences-but-different-results-dada2-vs-merged/34107 "2026-04-07T06:38:15Z")
Dear supporters, I’m relatively new to QIIME2, so apoplogies if I’m missing something obvious. I’m working with fungal ITS2 data and ran into an issue during taxonomic classification with feature-classifier classify-sk… --- ## [MIMt database for 16S, 18S, ITS, 23S and 28S new release available (March 26)](https://forum.qiime2.org/t/mimt-database-for-16s-18s-its-23s-and-28s-new-release-available-march-26/34069)
**Author:** [@A\_Munoz](https://forum.qiime2.org/u/A_Munoz)\ **Replies:** 0\ **Last updated:** [March 18, 2026, 7:20pm UTC](https://forum.qiime2.org/t/mimt-database-for-16s-18s-its-23s-and-28s-new-release-available-march-26/34069 "2026-03-18T19:20:10Z")
MIMt database new version has been released (March 26). Now every marker database contains thousands of new species well identified at every taxonomic level. Each database counts with two versions, one only containing se… --- ## [Integrating V3-V4 and V4 16S datasets for large-scale meta-analysis: Is Greengenes2 the optimal choice for cross-region alignment?](https://forum.qiime2.org/t/integrating-v3-v4-and-v4-16s-datasets-for-large-scale-meta-analysis-is-greengenes2-the-optimal-choice-for-cross-region-alignment/33938)
**Author:** [@wh466689](https://forum.qiime2.org/u/wh466689)\ **Replies:** 1\ **Last updated:** [March 6, 2026, 4:44pm UTC](https://forum.qiime2.org/t/integrating-v3-v4-and-v4-16s-datasets-for-large-scale-meta-analysis-is-greengenes2-the-optimal-choice-for-cross-region-alignment/33938 "2026-03-06T16:44:00Z")
Context & Motivation I am currently working on a large-scale meta-analysis involving hundreds of projects and over 10,000 samples. My dataset is a mixture of: V3-V4 region (e.g., amplicons from 341F/805R) V4 region (… --- ## [QIIME2-amplicon-2025.7 16S PacBio classification issues/discussion](https://forum.qiime2.org/t/qiime2-amplicon-2025-7-16s-pacbio-classification-issues-discussion/33999)
**Author:** [@ankurnaqib](https://forum.qiime2.org/u/ankurnaqib)\ **Replies:** 6\ **Last updated:** [February 24, 2026, 9:48pm UTC](https://forum.qiime2.org/t/qiime2-amplicon-2025-7-16s-pacbio-classification-issues-discussion/33999 "2026-02-24T21:48:47Z")
Hi, Apologies in advance for the long post. So I recently tried the GTDB226 classifier for the PacBio 16S full-length data. I am using the qiime2-amplicon-2025.7 version. Based on this reference - How to train a GTDB SS… --- ## [Best practice to identify mitochondria and chloroplasts using Greengenes2 2024.09](https://forum.qiime2.org/t/best-practice-to-identify-mitochondria-and-chloroplasts-using-greengenes2-2024-09/33955)
**Author:** [@Chumei\_Tang](https://forum.qiime2.org/u/Chumei_Tang)\ **Replies:** 2\ **Last updated:** [February 4, 2026, 1:23pm UTC](https://forum.qiime2.org/t/best-practice-to-identify-mitochondria-and-chloroplasts-using-greengenes2-2024-09/33955 "2026-02-04T13:23:12Z")
Hi everyone, There have been several posts in this forum outlining a current limitation of using Greengenes2: it lacks annotations of mitochondria or chloroplasts (at least until 2022.10). If I understood correctly, in … --- ## [No "Unclassified" etc taxa detected with grep in multiple unfiltered UNITE dbs?](https://forum.qiime2.org/t/no-unclassified-etc-taxa-detected-with-grep-in-multiple-unfiltered-unite-dbs/33917)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 1\ **Last updated:** [January 19, 2026, 12:12am UTC](https://forum.qiime2.org/t/no-unclassified-etc-taxa-detected-with-grep-in-multiple-unfiltered-unite-dbs/33917 "2026-01-19T00:12:48Z")
Hi Qiime2 community, :qiime2: :hot\_beverage: I am new to qiime2 and ITS analysis. I am running qiime2-amplicon-2025.7 in conda. Following recommendations on the qiime2 forum, I chose the developer version of the latest… --- ## [The differences in taxonomy output by the feature-classifier trainer and the full-length trainer](https://forum.qiime2.org/t/the-differences-in-taxonomy-output-by-the-feature-classifier-trainer-and-the-full-length-trainer/33911)
**Author:** [@CWZ](https://forum.qiime2.org/u/CWZ)\ **Replies:** 6\ **Last updated:** [January 18, 2026, 9:13am UTC](https://forum.qiime2.org/t/the-differences-in-taxonomy-output-by-the-feature-classifier-trainer-and-the-full-length-trainer/33911 "2026-01-18T09:13:37Z")
Hi guys, When I used the unite database to annotate the ITS results, why did the taxonomy table annotated by the classifier trained with primer (ITS1F 5'-CTTGGTCATTTAGAGGAAGTAA-3' ITS2R 5'-GCTGCGTTCTTCATCGATGC-3') differ… --- ## ["over-classification" of ASV taxonomy?](https://forum.qiime2.org/t/over-classification-of-asv-taxonomy/33898)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 2\ **Last updated:** [January 9, 2026, 6:14pm UTC](https://forum.qiime2.org/t/over-classification-of-asv-taxonomy/33898 "2026-01-09T18:14:26Z")
Happy New Year Qiime Community! :tada: I'm new to qiime2 and to DADA2 and to analyzing ITS data. :baby: I'm running qiime2-amplicon-2025.7 in a conda environment. Based on qiime2 forum recommendations, I'm using a UNIT… --- ## [guidance using quality-control evaluate-taxonomy and evaluate-composition](https://forum.qiime2.org/t/guidance-using-quality-control-evaluate-taxonomy-and-evaluate-composition/33862)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 8\ **Last updated:** [December 19, 2025, 5:02am UTC](https://forum.qiime2.org/t/guidance-using-quality-control-evaluate-taxonomy-and-evaluate-composition/33862 "2025-12-19T05:02:15Z")
Greetings Qiime2 community, :desktop\_computer: :hot\_beverage: I'm new to Qiime2, using qiime2-amplicon-2025.7 to test my ITS amplicon analysis pipeline with some mock libraries. What I want to do is use evaluate-taxono… --- ## [How to perform SILVA V3 classifier training?](https://forum.qiime2.org/t/how-to-perform-silva-v3-classifier-training/33790)
**Author:** [@Qiime2\_user](https://forum.qiime2.org/u/Qiime2_user)\ **Replies:** 9\ **Last updated:** [November 17, 2025, 7:55pm UTC](https://forum.qiime2.org/t/how-to-perform-silva-v3-classifier-training/33790 "2025-11-17T19:55:51Z")
Hi everyone, I’m trying to run taxonomy classification using the SILVA V3 classifier (for forward read only analysis), but I keep running into a scikit-learn version mismatch error in QIIME2-amplicon-2025.7. Here is the … --- ## [Troubleshoot classification where all ASVs are unassigned?](https://forum.qiime2.org/t/troubleshoot-classification-where-all-asvs-are-unassigned/33831)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 7\ **Last updated:** [December 2, 2025, 4:45pm UTC](https://forum.qiime2.org/t/troubleshoot-classification-where-all-asvs-are-unassigned/33831 "2025-12-02T16:45:40Z")
Hello Qiime Community, :seedling: I am running qiime2-amplicon-2025.7, using a mock library of fungi to benchmark my ITS amplicon analysis pipeline. This is my first time using Qiime2. I used RESCRIPt to curate a cu… --- ## [Issue with UNITE classifier for ITS1](https://forum.qiime2.org/t/issue-with-unite-classifier-for-its1/33837)
**Author:** [@mhog](https://forum.qiime2.org/u/mhog)\ **Replies:** 1\ **Last updated:** [December 2, 2025, 4:25pm UTC](https://forum.qiime2.org/t/issue-with-unite-classifier-for-its1/33837 "2025-12-02T16:25:54Z")
Hi there, I’m trying to assign taxonomy to my fungal ITS1 data using a pre-trained UNITE classifier. I’m using QIIME 2 version 2025.10 and conda (miniconda). I was having issues running ITSxpress with my paired-end data… --- ## [Evaluate custom taxonomic classifier with RESCRIPt?](https://forum.qiime2.org/t/evaluate-custom-taxonomic-classifier-with-rescript/33813)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 5\ **Last updated:** [November 27, 2025, 5:41am UTC](https://forum.qiime2.org/t/evaluate-custom-taxonomic-classifier-with-rescript/33813 "2025-11-27T05:41:23Z")
Greetings Q2 and RESCRIPt community, :globe\_showing\_europe\_africa: I am using qiime2-amplicon-2025.7, and am new to qiime2. I am analyzing ITS1 amplicon metagenomic data from MiSeq Illumina runs. I am benchmarking my p… --- ## [Exciting News: New QIIME 2 Tutorial on Arbuscular Mycorrhizal Fungi (AMF) Analysis Now Available!](https://forum.qiime2.org/t/exciting-news-new-qiime-2-tutorial-on-arbuscular-mycorrhizal-fungi-amf-analysis-now-available/33762)
**Author:** [@Manju\_M\_Gupta](https://forum.qiime2.org/u/Manju_M_Gupta)\ **Replies:** 0\ **Last updated:** [November 4, 2025, 6:10am UTC](https://forum.qiime2.org/t/exciting-news-new-qiime-2-tutorial-on-arbuscular-mycorrhizal-fungi-amf-analysis-now-available/33762 "2025-11-04T06:10:20Z")
Dear QIIME Community, I’m pleased to share that our AMF Tutorial - Step-by-Step Guide for Analyzing Arbuscular Mycorrhizal Fungal Communities using QIIME 2 has been officially released! The tutorial provides a complete… --- ## [MIMt database new release!!! QIIME2 classifiers for markers 16S, ITS, 18S, 23S and 28S](https://forum.qiime2.org/t/mimt-database-new-release-qiime2-classifiers-for-markers-16s-its-18s-23s-and-28s/33758)
**Author:** [@A\_Munoz](https://forum.qiime2.org/u/A_Munoz)\ **Replies:** 0\ **Last updated:** [November 3, 2025, 7:16am UTC](https://forum.qiime2.org/t/mimt-database-new-release-qiime2-classifiers-for-markers-16s-its-18s-23s-and-28s/33758 "2025-11-03T07:16:26Z")
A new version for MIMt database have been released. MIMt contains from 500 to 1500 new species in each of the ribosomal markers (for prokaryotes and eukaryotes). Every sequence in the database is full-length and redund… --- ## [confidence filtering pre or post classifier?](https://forum.qiime2.org/t/confidence-filtering-pre-or-post-classifier/33737)
**Author:** [@kbmac](https://forum.qiime2.org/u/kbmac)\ **Replies:** 3\ **Last updated:** [October 30, 2025, 8:41pm UTC](https://forum.qiime2.org/t/confidence-filtering-pre-or-post-classifier/33737 "2025-10-30T20:41:11Z")
Hello all! I’m at the point in my pipeline of assigning taxonomy to my sample of ITS sequences and filtering. I used a UNITE classifier generously provided by Colin Brislawn, and subsequently would like to filter the se… --- ## [Train PR2 Classifier](https://forum.qiime2.org/t/train-pr2-classifier/33701)
**Author:** [@Victoria92](https://forum.qiime2.org/u/Victoria92)\ **Replies:** 3\ **Last updated:** [October 20, 2025, 5:38pm UTC](https://forum.qiime2.org/t/train-pr2-classifier/33701 "2025-10-20T17:38:16Z")
I don’t know if I can bring this up here, I’m new using qiime environment and working with taxonomic data. I am working with 18S data and trying to train my classifier using PR2 database and assign taxonomy to my data b… [Next page](https://forum.qiime2.org/tag/taxonomy/29.md?match_all_tags=true&page=1&tags%5B%5D=taxonomy)