# \#fungi **URL:** https://forum.qiime2.org/tag/fungi/107.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [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… --- ## [Can I create one OTU table from mixed ITS1, ITS2, and full ITS fungal datasets?](https://forum.qiime2.org/t/can-i-create-one-otu-table-from-mixed-its1-its2-and-full-its-fungal-datasets/34157)
**Author:** [@budixin36](https://forum.qiime2.org/u/budixin36)\ **Replies:** 5\ **Last updated:** [May 6, 2026, 6:08pm UTC](https://forum.qiime2.org/t/can-i-create-one-otu-table-from-mixed-its1-its2-and-full-its-fungal-datasets/34157 "2026-05-06T18:08:52Z")
Hi QIIME 2 community, I am working on a fungal ITS meta-analysis using data from 77 BioProjects. The data include Illumina paired-end reads and Ion Torrent, GridION, and PacBio single-end reads. The datasets target diffe… --- ## [mixed orientation, dual-indexed, demultiplexed samples](https://forum.qiime2.org/t/mixed-orientation-dual-indexed-demultiplexed-samples/33428)
**Author:** [@skfagervols](https://forum.qiime2.org/u/skfagervols)\ **Replies:** 1\ **Last updated:** [July 11, 2025, 5:36pm UTC](https://forum.qiime2.org/t/mixed-orientation-dual-indexed-demultiplexed-samples/33428 "2025-07-11T17:36:02Z")
Hi So I have the dreaded dual indexed, mixed orientation (but demultiplexed) data. I am having trouble with the fungal sequences. I was able to deal with the mixed orientation on the 16S rRNA data since I could run th… --- ## [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… --- ## [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 … --- ## [qiime2 files to FUNguild](https://forum.qiime2.org/t/qiime2-files-to-funguild/28233)
**Author:** [@jrojas](https://forum.qiime2.org/u/jrojas)\ **Replies:** 1\ **Last updated:** [November 14, 2023, 6:00pm UTC](https://forum.qiime2.org/t/qiime2-files-to-funguild/28233 "2023-11-14T18:00:50Z")
Hello all! I'm running my first time pipeline on my dataset on qiime2 (working with fungal ITS sequences). I'm trying to use the software FUNguild to infer the role of my fungi in the microbiome of the plant they come f… --- ## [What is the meaning of "Other" category produced within UNITE+INSD all eukaryote using UCLUST](https://forum.qiime2.org/t/what-is-the-meaning-of-other-category-produced-within-unite-insd-all-eukaryote-using-uclust/27235)
**Author:** [@Doongsil](https://forum.qiime2.org/u/Doongsil)\ **Replies:** 1\ **Last updated:** [July 29, 2023, 1:56am UTC](https://forum.qiime2.org/t/what-is-the-meaning-of-other-category-produced-within-unite-insd-all-eukaryote-using-uclust/27235 "2023-07-29T01:56:33Z")
Hello! I'm analyzing nasopharyngeal mycobiome in patients. Wthin UNITE+INSD DB using UCLUST, does "Other" mean ambiguity? (can't decide between distinct taxa) I know "unidentifed" is present in DB, not taxonomically… --- ## [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… --- ## [Integrate fungal qPCR and composition results](https://forum.qiime2.org/t/integrate-fungal-qpcr-and-composition-results/23222)
**Author:** [@qwcheng](https://forum.qiime2.org/u/qwcheng)\ **Replies:** 1\ **Last updated:** [June 2, 2022, 1:04pm UTC](https://forum.qiime2.org/t/integrate-fungal-qpcr-and-composition-results/23222 "2022-06-02T13:04:57Z")
Hi all, I'm planning to analyze fungal microbiome composition in my samples but was wondering if I should sequence 18S or ITS. We have run a prelim qPCR test targeting 18S to quantify total fungi, using the method here … --- ## [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… --- ## [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… --- ## [Fungal ITS sequence from Illumina returns many unclassified reads](https://forum.qiime2.org/t/fungal-its-sequence-from-illumina-returns-many-unclassified-reads/20864)
**Author:** [@linjie\_0911](https://forum.qiime2.org/u/linjie_0911)\ **Replies:** 2\ **Last updated:** [September 26, 2021, 4:46am UTC](https://forum.qiime2.org/t/fungal-its-sequence-from-illumina-returns-many-unclassified-reads/20864 "2021-09-26T04:46:58Z")
Hi all, I did a fungi community analysis with DNA extracted from food waste. It was sequenced with Illumina platform using ITS1&2. Then I used Qiime 2 with SILVA132\_99 gene database and UNITE 8.2 taxonomy database to c… --- ## [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. … --- ## [classifier for fungi data analysis](https://forum.qiime2.org/t/classifier-for-fungi-data-analysis/19471)
**Author:** [@AnaBanana](https://forum.qiime2.org/u/AnaBanana)\ **Replies:** 2\ **Last updated:** [May 20, 2021, 10:10am UTC](https://forum.qiime2.org/t/classifier-for-fungi-data-analysis/19471 "2021-05-20T10:10:04Z")
Hello everyone, I am trying to analyse data from fungi from the genus Fusarium, I used the primers Fa 150 and Ra-2 to amplify 430bp of the elongation factor as done in Cobo-Diaz et al., 2019 (doi: 10.1093/femsec/fiz084… --- ## [Exporting processed .qza reads into separate .fasta files for each sample](https://forum.qiime2.org/t/exporting-processed-qza-reads-into-separate-fasta-files-for-each-sample/19327)
**Author:** [@sjcochran](https://forum.qiime2.org/u/sjcochran)\ **Replies:** 2\ **Last updated:** [April 24, 2021, 4:57pm UTC](https://forum.qiime2.org/t/exporting-processed-qza-reads-into-separate-fasta-files-for-each-sample/19327 "2021-04-24T16:57:11Z")
Hello! I am looking for help with processing my data from Fungal ITS1 amplicon sequencing. I have demultiplexed, paired-end reads in .fastq format. I imported my data into QIIME2 (installed on a VirtualBox), cut the pri… --- ## [Taxonomic assignment with UNITE database: most reads classified as "s\_\_unidentified"](https://forum.qiime2.org/t/taxonomic-assignment-with-unite-database-most-reads-classified-as-s-unidentified/18696)
**Author:** [@Danilo\_Reis](https://forum.qiime2.org/u/Danilo_Reis)\ **Replies:** 6\ **Last updated:** [March 10, 2021, 10:19am UTC](https://forum.qiime2.org/t/taxonomic-assignment-with-unite-database-most-reads-classified-as-s-unidentified/18696 "2021-03-10T10:19:09Z")
Hi everyone, I am for the first time using Qiime2 to analyze ITS data (Illumina Miseq V3 - 300 bp paired-end reads) for fungal endophytes diversity in plant roots. I received different folders from the sequencing facil… --- ## [Fungi taxonomic analysis](https://forum.qiime2.org/t/fungi-taxonomic-analysis/15749)
**Author:** [@elolimy](https://forum.qiime2.org/u/elolimy)\ **Replies:** 24\ **Last updated:** [August 1, 2020, 5:21pm UTC](https://forum.qiime2.org/t/fungi-taxonomic-analysis/15749 "2020-08-01T17:21:59Z")
Guys, I have used the code below to perform taxonomic analysis for ITS fungi data against unite-ver7-99-classifier-01.12.2017.qza database using qiime2-2020.2 qiime feature-classifier classify-sklearn --i-classifier … --- ## [ITS classification - nothing beyond phylum level](https://forum.qiime2.org/t/its-classification-nothing-beyond-phylum-level/15022)
**Author:** [@spongebob](https://forum.qiime2.org/u/spongebob)\ **Replies:** 6\ **Last updated:** [June 6, 2020, 2:20am UTC](https://forum.qiime2.org/t/its-classification-nothing-beyond-phylum-level/15022 "2020-06-06T02:20:16Z")
Hi there, I recently migrated over to qiime2 from mothur. I am processing the same ITS sequence data, that i did with mothur and i am using the same UNITE database for ITS classification. When i used the mothur pipeli… --- ## [q2-itsxpress creates incomplete manifest after trim-pair-output-unmerged](https://forum.qiime2.org/t/q2-itsxpress-creates-incomplete-manifest-after-trim-pair-output-unmerged/10243)
**Author:** [@etmmaas](https://forum.qiime2.org/u/etmmaas)\ **Replies:** 3\ **Last updated:** [June 14, 2019, 8:28pm UTC](https://forum.qiime2.org/t/q2-itsxpress-creates-incomplete-manifest-after-trim-pair-output-unmerged/10243 "2019-06-14T20:28:15Z")
Hi, I have been using q2-itsxpress to extract the its2 region before running dada2. The qiime itsxpress trim-pair-output-unmerged seems to work fine, but the output gives .qza files where the manifest file only contains… --- ## [Merging (or not) ITS2 amplicons with variable length](https://forum.qiime2.org/t/merging-or-not-its2-amplicons-with-variable-length/7868)
**Author:** [@rahel\_park](https://forum.qiime2.org/u/rahel_park)\ **Replies:** 16\ **Last updated:** [January 25, 2019, 1:10pm UTC](https://forum.qiime2.org/t/merging-or-not-its2-amplicons-with-variable-length/7868 "2019-01-25T13:10:06Z")
Hi! I am trying to analyze the fungal amplicons, but I have troubles to find an optimal way to do it. The primers used - ITS86F/ITS4 MiSeq 2x300 (qiime2-2018.11, conda installation) In my pipeline I import the seque… --- ## [Metaphlan2 vs vsearch for fungal metagenomic shotgun sequences](https://forum.qiime2.org/t/metaphlan2-vs-vsearch-for-fungal-metagenomic-shotgun-sequences/6536)
**Author:** [@haydenbs](https://forum.qiime2.org/u/haydenbs)\ **Replies:** 8\ **Last updated:** [November 20, 2018, 1:47pm UTC](https://forum.qiime2.org/t/metaphlan2-vs-vsearch-for-fungal-metagenomic-shotgun-sequences/6536 "2018-11-20T13:47:11Z")
Hey, I'm fairly new to bioinformatics and I am working with a professor on fungal metagenomic shotgun sequences and am trying to use these reads to find the composition of the fungal diversity at (the preferred minimum)… --- ## [Assigning guild to ITS data in OTU table](https://forum.qiime2.org/t/assigning-guild-to-its-data-in-otu-table/5418)
**Author:** [@Fabs](https://forum.qiime2.org/u/Fabs)\ **Replies:** 0\ **Last updated:** [August 6, 2018, 12:52am UTC](https://forum.qiime2.org/t/assigning-guild-to-its-data-in-otu-table/5418 "2018-08-06T00:52:19Z")
Hi, I have a quick question but by looking through the forum, I feel like I already know the answer but I would just like to verify. I have created and exported the OTU table to work in R, when I remembered that I need… --- ## [Is there a flowchart for fungi analysis!](https://forum.qiime2.org/t/is-there-a-flowchart-for-fungi-analysis/3303)
**Author:** [@hzh0005](https://forum.qiime2.org/u/hzh0005)\ **Replies:** 3\ **Last updated:** [March 5, 2018, 3:08pm UTC](https://forum.qiime2.org/t/is-there-a-flowchart-for-fungi-analysis/3303 "2018-03-05T15:08:23Z")
As the current exaples are shown how to process bacterial data, can anyone give a flowchart to analyze fungi data? Thanks! --- ## [Qiime database for fungi sequencing in ITS1](https://forum.qiime2.org/t/qiime-database-for-fungi-sequencing-in-its1/3298)
**Author:** [@hzh0005](https://forum.qiime2.org/u/hzh0005)\ **Replies:** 2\ **Last updated:** [March 5, 2018, 3:01pm UTC](https://forum.qiime2.org/t/qiime-database-for-fungi-sequencing-in-its1/3298 "2018-03-05T15:01:29Z")
Would you please provide a qiime database for ITS classification? Thanks! --- ## [Kingdom-level classification of fungal ITS sequences](https://forum.qiime2.org/t/kingdom-level-classification-of-fungal-its-sequences/2588)
**Author:** [@bsen2018](https://forum.qiime2.org/u/bsen2018)\ **Replies:** 1\ **Last updated:** [January 16, 2018, 5:18pm UTC](https://forum.qiime2.org/t/kingdom-level-classification-of-fungal-its-sequences/2588 "2018-01-16T17:18:33Z")
Hi @Nicholas\_Bokulich, I am in a similar problem with the fungal sequences, getting only up to kingdom and phyla level classification. Thus, in continuation to the earlier threads, I would like to request your help on t… --- ## [Fungal ITS classification with UNITE database](https://forum.qiime2.org/t/fungal-its-classification-with-unite-database/2003)
**Author:** [@Hillary\_Smith](https://forum.qiime2.org/u/Hillary_Smith)\ **Replies:** 8\ **Last updated:** [January 10, 2018, 9:25pm UTC](https://forum.qiime2.org/t/fungal-its-classification-with-unite-database/2003 "2018-01-10T21:25:11Z")
Hi qiime2 forum, I am attempting to analyze a dataset generated from fungal ITS sequences, and have run into similar issues as the following two threads, however haven't been able to solve my problem with the advice the… --- ## [Does the pretrained classifer silva-119-99-nb-classifier detect fungi?](https://forum.qiime2.org/t/does-the-pretrained-classifer-silva-119-99-nb-classifier-detect-fungi/1907)
**Author:** [@mamillerpa](https://forum.qiime2.org/u/mamillerpa)\ **Replies:** 1\ **Last updated:** [November 21, 2017, 12:41am UTC](https://forum.qiime2.org/t/does-the-pretrained-classifer-silva-119-99-nb-classifier-detect-fungi/1907 "2017-11-21T00:41:46Z")
Wow, I've been getting a lot of great help form this forum! Does the classifier at https://data.qiime2.org/2017.10/common/silva-119-99-nb-classifier.qza detect fungi based on their 18S SSU, or just bacteria bused on th… --- ## [ITS import issues](https://forum.qiime2.org/t/its-import-issues/1674)
**Author:** [@morganpuff](https://forum.qiime2.org/u/morganpuff)\ **Replies:** 2\ **Last updated:** [October 31, 2017, 4:22pm UTC](https://forum.qiime2.org/t/its-import-issues/1674 "2017-10-31T16:22:58Z")
Hello, I have completed my 16s run which contains files used in the Paired End Fastq Phred 33 format- and worked. I am now working on my ITS run, which contained similar file types as my 16s run and tried to import usin… --- ## [Should I truncate all sequences to the same length for doing ITS?](https://forum.qiime2.org/t/should-i-truncate-all-sequences-to-the-same-length-for-doing-its/1521)
**Author:** [@hongwei2017](https://forum.qiime2.org/u/hongwei2017)\ **Replies:** 3\ **Last updated:** [October 18, 2017, 12:17am UTC](https://forum.qiime2.org/t/should-i-truncate-all-sequences-to-the-same-length-for-doing-its/1521 "2017-10-18T00:17:06Z")
Dear Qiime team, Thanks first for all your unfailing supports! Before doing the taxonomy for ITS, should I truncate all my sequences to the same length before using the classifier? Because I heard that when people usin…