# \#its **URL:** https://forum.qiime2.org/tag/its/72.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Is ANCOM-BC2 the best choice for my data?](https://forum.qiime2.org/t/is-ancom-bc2-the-best-choice-for-my-data/34294)
**Author:** [@kranderson](https://forum.qiime2.org/u/kranderson)\ **Replies:** 2\ **Last updated:** [September 1, 2026, 6:03am UTC](https://forum.qiime2.org/t/is-ancom-bc2-the-best-choice-for-my-data/34294 "2026-09-01T06:03:31Z")
My study is comparing the fungal diversity between soil that experienced a wildfire (NoRxF) between soil that was treated with prescribed fire prior to experiencing the wildfire (RxF). It's a paired study design where 6 … --- ## [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… --- ## [ASV vs OTU for fungal ITS](https://forum.qiime2.org/t/asv-vs-otu-for-fungal-its/30735)
**Author:** [@Saptarathi\_Deb](https://forum.qiime2.org/u/Saptarathi_Deb)\ **Replies:** 11\ **Last updated:** [August 30, 2026, 5:37pm UTC](https://forum.qiime2.org/t/asv-vs-otu-for-fungal-its/30735 "2026-08-30T17:37:55Z")
Hello Everyone, I am searching for some more clarity about the use of ASV or OTU for fungal ITS analysis. After going through many publications I am seeing comments against the use of ASV for fungal ITS where the main … --- ## [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! … --- ## [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… --- ## [Fungal primer choice avoiding plant amplification](https://forum.qiime2.org/t/fungal-primer-choice-avoiding-plant-amplification/33960)
**Author:** [@Daniel\_Angulo](https://forum.qiime2.org/u/Daniel_Angulo)\ **Replies:** 2\ **Last updated:** [February 8, 2026, 9:46pm UTC](https://forum.qiime2.org/t/fungal-primer-choice-avoiding-plant-amplification/33960 "2026-02-08T21:46:27Z")
Hi all, I’m working on a PhD project focused on fungal communities in dung samples from herbivorous birds (ptarmigan and geese) and need advice on selecting fungal-specific primers. The plan is to use Illumina sequencin… --- ## [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… --- ## [Shotgun sequencing of Fungi - UNITE or KRAKEN2](https://forum.qiime2.org/t/shotgun-sequencing-of-fungi-unite-or-kraken2/33291)
**Author:** [@FRANCESCOMONTESI](https://forum.qiime2.org/u/FRANCESCOMONTESI)\ **Replies:** 1\ **Last updated:** [June 11, 2025, 8:29pm UTC](https://forum.qiime2.org/t/shotgun-sequencing-of-fungi-unite-or-kraken2/33291 "2025-06-11T20:29:55Z")
Hi everybody, i have fastQ files produced by shotgun DNA sequencing (paired-end) performed with illumina platform. I have sequenced 3 fungi in monocolture, so i have 3 samples, i expect 3 different species. I have 2 qu… --- ## [Request for Pre-trained UNITE Classifier (ITS1)](https://forum.qiime2.org/t/request-for-pre-trained-unite-classifier-its1/33066)
**Author:** [@mleon](https://forum.qiime2.org/u/mleon)\ **Replies:** 3\ **Last updated:** [April 30, 2025, 7:09pm UTC](https://forum.qiime2.org/t/request-for-pre-trained-unite-classifier-its1/33066 "2025-04-30T19:09:08Z")
Hi everyone, I'm following the ITSxpress tutorial (Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences) and trying to use the classifier.qza file mentioned there as a pre-trained classifier. However, when… --- ## [ITS, 18S, 23S and 28S new reference databases to use in QIIME2](https://forum.qiime2.org/t/its-18s-23s-and-28s-new-reference-databases-to-use-in-qiime2/33018)
**Author:** [@A\_Munoz](https://forum.qiime2.org/u/A_Munoz)\ **Replies:** 0\ **Last updated:** [April 17, 2025, 1:37pm UTC](https://forum.qiime2.org/t/its-18s-23s-and-28s-new-reference-databases-to-use-in-qiime2/33018 "2025-04-17T13:37:07Z")
MIMt database has grown and now it includes databases for other markers like ITS, 18S, 23S and 28S to the previous 16S already in use. All the databases have two versions, one with only curated sequences from Target Loc… --- ## [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… --- ## [choice of fungal primers](https://forum.qiime2.org/t/choice-of-fungal-primers/25731)
**Author:** [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Replies:** 13\ **Last updated:** [December 9, 2024, 4:25pm UTC](https://forum.qiime2.org/t/choice-of-fungal-primers/25731 "2024-12-09T16:25:41Z")
Hi all, I'm getting ready to place an order for barcoded primers that will be used for Illumina sequencing of host-associated and non-host-associated fungal communities. After doing some research on primers, I'm leaning… --- ## [fungal ITS analysis with QIIME2: current recommended workflow?](https://forum.qiime2.org/t/fungal-its-analysis-with-qiime2-current-recommended-workflow/30809)
**Author:** [@Rob\_DNA](https://forum.qiime2.org/u/Rob_DNA)\ **Replies:** 6\ **Last updated:** [July 22, 2024, 12:07pm UTC](https://forum.qiime2.org/t/fungal-its-analysis-with-qiime2-current-recommended-workflow/30809 "2024-07-22T12:07:17Z")
Hello, I'm working with fungal ITS sequencing for the first time and I notice that there is not a general consensus on which work flow to use, in the context of short-read sequencing such as Illumina sequencing. Especia… --- ## [Taxa collapse shows too general taxonomic assignations](https://forum.qiime2.org/t/taxa-collapse-shows-too-general-taxonomic-assignations/30526)
**Author:** [@salias](https://forum.qiime2.org/u/salias)\ **Replies:** 11\ **Last updated:** [June 20, 2024, 2:20pm UTC](https://forum.qiime2.org/t/taxa-collapse-shows-too-general-taxonomic-assignations/30526 "2024-06-20T14:20:18Z")
I'm collapsing my feature table by family taxonomic level prior to running ANCOM-BC. I generated the QZV from the QZA collapsed table, and I found that there is a too general taxonomic assignation with a really high frec… --- ## [Issues with taxonomic classification UNITE 9.0 and 10.0](https://forum.qiime2.org/t/issues-with-taxonomic-classification-unite-9-0-and-10-0/30402)
**Author:** [@mica.tosi](https://forum.qiime2.org/u/mica.tosi)\ **Replies:** 2\ **Last updated:** [June 6, 2024, 8:19am UTC](https://forum.qiime2.org/t/issues-with-taxonomic-classification-unite-9-0-and-10-0/30402 "2024-06-06T08:19:48Z")
Hello QIIME2 team :wave: We wanted to share some issues we’ve been having with recent UNITE classifiers for fungal ITS. We found someone with a similar problem in a closed discussion, but unfortunately that information … --- ## [Which version of UNITE database should I choose?](https://forum.qiime2.org/t/which-version-of-unite-database-should-i-choose/12049)
**Author:** [@sixvable](https://forum.qiime2.org/u/sixvable)\ **Replies:** 2\ **Last updated:** [February 23, 2024, 8:03pm UTC](https://forum.qiime2.org/t/which-version-of-unite-database-should-i-choose/12049 "2024-02-23T20:03:28Z")
Recently I have been trying to analysis my ITS amplicon sequences data and I found a little bit confusing thing about the Unite database. On the Unite database they have distributed two different type of fungi unite dat… --- ## [Training an ITS classifier](https://forum.qiime2.org/t/training-an-its-classifier/29100)
**Author:** [@Beh\_Yaad](https://forum.qiime2.org/u/Beh_Yaad)\ **Replies:** 15\ **Last updated:** [February 14, 2024, 9:45pm UTC](https://forum.qiime2.org/t/training-an-its-classifier/29100 "2024-02-14T21:45:49Z")
Hi everyone! I'm a bit puzzled about training the classifier, and I'd really appreciate your help. I followed the "Training feature classifiers with q2-feature-classifier" tutorial to train an ITS classifier. I should… --- ## [Merging ITS1 & ITS2 primers: a question about methods](https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142)
**Author:** [@Antani](https://forum.qiime2.org/u/Antani)\ **Replies:** 2\ **Last updated:** [February 4, 2024, 12:02am UTC](https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142 "2024-02-04T00:02:50Z")
Dear Qiime2 community, I have a question about a data analyses procedure. I have a set of 500 samples from whom ITS1 and ITS2 have been amplified. I've analyzed them without merging these two dataset because I read th… --- ## [large ITS dataset](https://forum.qiime2.org/t/large-its-dataset/28695)
**Author:** [@Sue](https://forum.qiime2.org/u/Sue)\ **Replies:** 1\ **Last updated:** [December 27, 2023, 7:45pm UTC](https://forum.qiime2.org/t/large-its-dataset/28695 "2023-12-27T19:45:40Z")
Hi, I have tested Qiime2 on a mock ITS dataset (DNA metabarcoding of a mock community of 189 fungal strains associated to plants and soils. - Omics). Subsequently, I applied Picrust2, and now I want to visualize the res… --- ## [ITS itsxpress trim-unmerged encounters problems](https://forum.qiime2.org/t/its-itsxpress-trim-unmerged-encounters-problems/27642)
**Author:** [@npj06](https://forum.qiime2.org/u/npj06)\ **Replies:** 1\ **Last updated:** [September 13, 2023, 4:52pm UTC](https://forum.qiime2.org/t/its-itsxpress-trim-unmerged-encounters-problems/27642 "2023-09-13T16:52:59Z")
Dear developers of ITSexpress, I would like to express my gratitude to you for creating such a powerful analysis tool. However, I have encountered some issues while using it, which have hindered my analysis progress. Fi… --- ## [q2-hitac: a plugin for taxonomic classification of fungal ITS sequences](https://forum.qiime2.org/t/q2-hitac-a-plugin-for-taxonomic-classification-of-fungal-its-sequences/25031)
**Author:** [@mirand863](https://forum.qiime2.org/u/mirand863)\ **Replies:** 0\ **Last updated:** [December 15, 2022, 4:10pm UTC](https://forum.qiime2.org/t/q2-hitac-a-plugin-for-taxonomic-classification-of-fungal-its-sequences/25031 "2022-12-15T16:10:28Z")
Have you ever had to perform taxonomic classification of fungal ITS sequences and were not happy with the results? Well, if you had this problem, I would like to invite you to try our hierarchical taxonomic classifier ca… --- ## [ITS extraction after joining paired-end reads?](https://forum.qiime2.org/t/its-extraction-after-joining-paired-end-reads/24298)
**Author:** [@gabt](https://forum.qiime2.org/u/gabt)\ **Replies:** 2\ **Last updated:** [October 13, 2022, 8:08am UTC](https://forum.qiime2.org/t/its-extraction-after-joining-paired-end-reads/24298 "2022-10-13T08:08:48Z")
I am quite new to the field of fungal amplicon analysis and I had many discussion whether to use DADA2 or Vsearch with OTU-based approach, to obtain the famous count table. As with all the things in bioinformatics there … --- ## [itsxpress - not fastq.gz format error](https://forum.qiime2.org/t/itsxpress-not-fastq-gz-format-error/23981)
**Author:** [@AAN\_Aseeri](https://forum.qiime2.org/u/AAN_Aseeri)\ **Replies:** 11\ **Last updated:** [October 6, 2022, 1:01am UTC](https://forum.qiime2.org/t/itsxpress-not-fastq-gz-format-error/23981 "2022-10-06T01:01:33Z")
version used: qiime2-2022.2 q2-itsxpress 1.8.0 pypi\_0 pypi itsxpress 1.8.0 pyhdfd78af\_2 bioconda bbmap 38.98 h5c4e… --- ## [Optimizing taxonomy assignment to reduce unassigned ITS reads](https://forum.qiime2.org/t/optimizing-taxonomy-assignment-to-reduce-unassigned-its-reads/22249)
**Author:** [@Sonja](https://forum.qiime2.org/u/Sonja)\ **Replies:** 3\ **Last updated:** [February 22, 2022, 11:40pm UTC](https://forum.qiime2.org/t/optimizing-taxonomy-assignment-to-reduce-unassigned-its-reads/22249 "2022-02-22T23:40:09Z")
Hello everyone, I'm analysing microbial communities in a fjord and got stuck with the taxonomy assignment of fungi, I get 25-90% unassigned reads in my samples. The amplicons were generated using ITS3 and ITS4 as primer… --- ## [Interpreting Unassigned/k\_Fungi ITS taxonomy generated using 3 reference datasets (UNITE & NCBI)](https://forum.qiime2.org/t/interpreting-unassigned-k-fungi-its-taxonomy-generated-using-3-reference-datasets-unite-ncbi/22202)
**Author:** [@ardorbel](https://forum.qiime2.org/u/ardorbel)\ **Replies:** 1\ **Last updated:** [February 17, 2022, 8:00am UTC](https://forum.qiime2.org/t/interpreting-unassigned-k-fungi-its-taxonomy-generated-using-3-reference-datasets-unite-ncbi/22202 "2022-02-17T08:00:58Z")
Hello, I'm currently comparing taxonomy results for ITS1 sequences derived from sediment samples (amplified using ITS1F/ITS2), obtained using three different naive-bayes classifiers (trained in qiime2) using the followi… --- ## [Large amount of 'Unassigned' ITS sequences in classify-consensus-blast results](https://forum.qiime2.org/t/large-amount-of-unassigned-its-sequences-in-classify-consensus-blast-results/21073)
**Author:** [@kelmermcunha](https://forum.qiime2.org/u/kelmermcunha)\ **Replies:** 7\ **Last updated:** [October 21, 2021, 8:25pm UTC](https://forum.qiime2.org/t/large-amount-of-unassigned-its-sequences-in-classify-consensus-blast-results/21073 "2021-10-21T20:25:04Z")
Hello everyone! :wave: Before anything, this is my first post in the QIIME2 Forum. I'm already sorry if this is not the right topic to place my questions. I'll try to provide most information as possible. With that out… --- ## [Data loss when trimming ITS](https://forum.qiime2.org/t/data-loss-when-trimming-its/20777)
**Author:** [@paulad](https://forum.qiime2.org/u/paulad)\ **Replies:** 3\ **Last updated:** [September 23, 2021, 7:33pm UTC](https://forum.qiime2.org/t/data-loss-when-trimming-its/20777 "2021-09-23T19:33:12Z")
Hi all, I am analyzing some ITS sequences using this tutorial and I have some questions regarding trimming. After creating the demux.qza file, I used the qiime cutadapt trim-paired command to cut the adapters and got th… --- ## [Fungi ITS taxonomy bar plot and relative frequency biom does not match in ratio](https://forum.qiime2.org/t/fungi-its-taxonomy-bar-plot-and-relative-frequency-biom-does-not-match-in-ratio/20796)
**Author:** [@linjie\_0911](https://forum.qiime2.org/u/linjie_0911)\ **Replies:** 6\ **Last updated:** [September 21, 2021, 10:52pm UTC](https://forum.qiime2.org/t/fungi-its-taxonomy-bar-plot-and-relative-frequency-biom-does-not-match-in-ratio/20796 "2021-09-21T22:52:01Z")
Hi all, I am running into some weird questions when I am doing fungi taxonomy work with Illumina result on Qiime 2. Fungi gene were sequenced on ITS1and 2 primer on Illumina platform. The result came back like this. … --- ## [Taxonomic assignment at the species level](https://forum.qiime2.org/t/taxonomic-assignment-at-the-species-level/20456)
**Author:** [@vetalinesantana](https://forum.qiime2.org/u/vetalinesantana)\ **Replies:** 2\ **Last updated:** [August 13, 2021, 10:52pm UTC](https://forum.qiime2.org/t/taxonomic-assignment-at-the-species-level/20456 "2021-08-13T22:52:21Z")
Hello everybody, I've heard that doing taxonomic assignments at the species level is not accurate. That's true? Does anyone have a scientific paper that discusses this? I used the classifier skylearn and UNITE and SILV… [Next page](https://forum.qiime2.org/tag/its/72.md?match_all_tags=true&page=1&tags%5B%5D=its)