# Latest **URL:** https://forum.qiime2.org/latest.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Frequent Questions and "Best of the QIIME 2 Forum"](https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608)
**Author:** [@q2d2](https://forum.qiime2.org/u/q2d2)\ **Replies:** 1\ **Last updated:** [February 20, 2020, 6:02am UTC](https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608 "2020-02-20T06:02:47Z")
The following is a list of frequently asked questions on the forum, with answers, to serve as a point of reference for forum users to quickly find answers, or for forum users and moderators to use as a reference when hel… --- ## [NCBI or SILVA for curating a custom 16S rDNA reference database?](https://forum.qiime2.org/t/ncbi-or-silva-for-curating-a-custom-16s-rdna-reference-database/34286)
**Author:** [@deClare125](https://forum.qiime2.org/u/deClare125)\ **Replies:** 12\ **Last updated:** [September 28, 2026, 6:20pm UTC](https://forum.qiime2.org/t/ncbi-or-silva-for-curating-a-custom-16s-rdna-reference-database/34286 "2026-09-28T18:20:51Z")
Hello all, I'm seeking advice on creating a 16S rDNA database for an avian diet metabarcoding project. I chose the primers 16S1F-degenerate and 16S2R-degenerate (Deagle et al 2007) alongside COI ANML primers to generate… --- ## [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… --- ## [Advice on Conducting a Targeted Pathogenic Species Search using ITS1 data using QIIME2 feature-classifier plugin](https://forum.qiime2.org/t/advice-on-conducting-a-targeted-pathogenic-species-search-using-its1-data-using-qiime2-feature-classifier-plugin/34336)
**Author:** [@vic.everhart](https://forum.qiime2.org/u/vic.everhart)\ **Replies:** 3\ **Last updated:** [September 24, 2026, 9:09pm UTC](https://forum.qiime2.org/t/advice-on-conducting-a-targeted-pathogenic-species-search-using-its1-data-using-qiime2-feature-classifier-plugin/34336 "2026-09-24T21:09:46Z")
Hello. I am currently working with ITS1 amplicon data and am new to QIIME2. I am interested in cross referencing my ITS1 data with a specifically curated database with fungal pathogens of interest. I'm interested in pote… --- ## [class-weight parameter for rescript-evaluate evaluate-fit-classifier function](https://forum.qiime2.org/t/class-weight-parameter-for-rescript-evaluate-evaluate-fit-classifier-function/34320)
**Author:** [@irvinng98](https://forum.qiime2.org/u/irvinng98)\ **Replies:** 3\ **Last updated:** [September 22, 2026, 9:00pm UTC](https://forum.qiime2.org/t/class-weight-parameter-for-rescript-evaluate-evaluate-fit-classifier-function/34320 "2026-09-22T21:00:32Z")
Hello, Previously I had used the qiime feature-classifier fit-classifier-naive-bayes function as the last step to create my classifier. This function allowed me to use --i-class-weight as an option for input. However, I… --- ## [Recommended QIIME 2 workflow for ONT full-length 16S data and integration of EMU results for alpha/beta diversity](https://forum.qiime2.org/t/recommended-qiime-2-workflow-for-ont-full-length-16s-data-and-integration-of-emu-results-for-alpha-beta-diversity/34335)
**Author:** [@dayanne09](https://forum.qiime2.org/u/dayanne09)\ **Replies:** 2\ **Last updated:** [September 22, 2026, 12:39pm UTC](https://forum.qiime2.org/t/recommended-qiime-2-workflow-for-ont-full-length-16s-data-and-integration-of-emu-results-for-alpha-beta-diversity/34335 "2026-09-22T12:39:21Z")
Hello. I am currently working with full-length 16S rRNA amplicon sequencing data generated with Oxford Nanopore Technologies (ONT), and I would really appreciate some guidance regarding the most appropriate workflow to p… --- ## [import multiplexed miseq single-end, barcodes in mapping file](https://forum.qiime2.org/t/import-multiplexed-miseq-single-end-barcodes-in-mapping-file/34333)
**Author:** [@Scott\_Kelley1](https://forum.qiime2.org/u/Scott_Kelley1)\ **Replies:** 1\ **Last updated:** [September 22, 2026, 3:30am UTC](https://forum.qiime2.org/t/import-multiplexed-miseq-single-end-barcodes-in-mapping-file/34333 "2026-09-22T03:30:04Z")
Version: qiime2-amplicon-2024.10 I have an older Illumina miSeq single-end dataset with NO barcodes.fastq.gz file. The barcodes are in the mapping file (see below). I searched the forums and I found the cutadapt code th… --- ## [PacBio DADA2-ccs plugin is losing lots of data](https://forum.qiime2.org/t/pacbio-dada2-ccs-plugin-is-losing-lots-of-data/34299)
**Author:** [@Prajina-N](https://forum.qiime2.org/u/Prajina-N)\ **Replies:** 6\ **Last updated:** [September 22, 2026, 3:03am UTC](https://forum.qiime2.org/t/pacbio-dada2-ccs-plugin-is-losing-lots-of-data/34299 "2026-09-22T03:03:27Z")
Howdy, I ran DADA2-ccs plugin for PacBio sequences for Bac16S but I am losing a lot of reads in filtering step. Search: sample-id #q2:types input numeric primer-removed numeric percentage of input primer-removed nu… --- ## [Gemelli Joint-RPCA biplot axis 1 is 100% ](https://forum.qiime2.org/t/gemelli-joint-rpca-biplot-axis-1-is-100/34334)
**Author:** [@Bark9299](https://forum.qiime2.org/u/Bark9299)\ **Replies:** 0\ **Last updated:** [September 21, 2026, 4:37pm UTC](https://forum.qiime2.org/t/gemelli-joint-rpca-biplot-axis-1-is-100/34334 "2026-09-21T16:37:17Z")
I am using qiime2-amplicon-2025.7 conda environment. I am following the Joint-RPCA tutorial on my shotgun metagenomic and 16S V4 shared samples. I used the following code to produce the volatility plot and biplot (My dat… --- ## [Installation error - unsolvable sortmerna issue](https://forum.qiime2.org/t/installation-error-unsolvable-sortmerna-issue/34297)
**Author:** [@desmodus1984](https://forum.qiime2.org/u/desmodus1984)\ **Replies:** 2\ **Last updated:** [September 21, 2026, 1:54pm UTC](https://forum.qiime2.org/t/installation-error-unsolvable-sortmerna-issue/34297 "2026-09-21T13:54:05Z")
Hi, A friend shared some fastq.gz files of 16S to compare communities across a river. I offered to analyze them,so I am trying to install qiime2 in conda, and it failed with error: conda env create --name qiime2 --fi… --- ## [High Read Loss Due to Poor Merging and Chimeras During DADA denoising](https://forum.qiime2.org/t/high-read-loss-due-to-poor-merging-and-chimeras-during-dada-denoising/34323)
**Author:** [@deClare125](https://forum.qiime2.org/u/deClare125)\ **Replies:** 9\ **Last updated:** [September 19, 2026, 2:54pm UTC](https://forum.qiime2.org/t/high-read-loss-due-to-poor-merging-and-chimeras-during-dada-denoising/34323 "2026-09-19T14:54:47Z")
Hi QIIME forum! I am currently stuck at the denoising phase, where my data has really low pair-end merging rates and lots of loss due to chimeras. I am a total newbie to metabarcoding so while I have read a lot of posts… --- ## [deseq2: rarefaction?](https://forum.qiime2.org/t/deseq2-rarefaction/34332)
**Author:** [@asmaamorsi](https://forum.qiime2.org/u/asmaamorsi)\ **Replies:** 1\ **Last updated:** [September 18, 2026, 8:06am UTC](https://forum.qiime2.org/t/deseq2-rarefaction/34332 "2026-09-18T08:06:35Z")
Hi everyone, When performing differential abundance analysis using DESeq2, should we use the unrarefied (raw) feature table, or should the feature table first be rarefied to the same sequencing depth used for alpha and … --- ## [Apple ending general Rosetta support in macOS 28 — what is the recommended path for QIIME 2 on Apple Silicon Macs?](https://forum.qiime2.org/t/apple-ending-general-rosetta-support-in-macos-28-what-is-the-recommended-path-for-qiime-2-on-apple-silicon-macs/34330)
**Author:** [@yonghyun09](https://forum.qiime2.org/u/yonghyun09)\ **Replies:** 1\ **Last updated:** [September 17, 2026, 2:57pm UTC](https://forum.qiime2.org/t/apple-ending-general-rosetta-support-in-macos-28-what-is-the-recommended-path-for-qiime-2-on-apple-silicon-macs/34330 "2026-09-17T14:57:47Z")
Hello QIIME 2 developers and community, I am currently using QIIME 2 on an Apple Silicon Mac (MacBook Pro with an M2 chip), and my current QIIME 2 environment is running through Rosetta using the osx-64 architecture. I… --- ## [QIIME 2 2026.10 environment files](https://forum.qiime2.org/t/qiime-2-2026-10-environment-files/34329)
**Author:** [@q2d2](https://forum.qiime2.org/u/q2d2)\ **Replies:** 0\ **Last updated:** [September 17, 2026, 7:51am UTC](https://forum.qiime2.org/t/qiime-2-2026-10-environment-files/34329 "2026-09-17T07:51:21Z")
Below is the list of guaranteed environment file updates for the 2026.10 QIIME 2 release. You can use the linked environment files for each distribution to ensure compatibility with any plugin you're developing against t… --- ## [Data Visualization Troubleshooting](https://forum.qiime2.org/t/data-visualization-troubleshooting/34327)
**Author:** [@ahsankaleem](https://forum.qiime2.org/u/ahsankaleem)\ **Replies:** 1\ **Last updated:** [September 17, 2026, 2:38am UTC](https://forum.qiime2.org/t/data-visualization-troubleshooting/34327 "2026-09-17T02:38:33Z")
Hello everyone! I hope that you are enjoying the best of health. I analysed my 16S data using QIIME2 pipeline. Although I have completed the data analysis, I could not generate publication quality figures using QIIME2 p… --- ## [using new from Silva 144 classifiers with qiime2-amplicon-2025.10](https://forum.qiime2.org/t/using-new-from-silva-144-classifiers-with-qiime2-amplicon-2025-10/34325)
**Author:** [@jack2017](https://forum.qiime2.org/u/jack2017)\ **Replies:** 4\ **Last updated:** [September 15, 2026, 1:57pm UTC](https://forum.qiime2.org/t/using-new-from-silva-144-classifiers-with-qiime2-amplicon-2025-10/34325 "2026-09-15T13:57:54Z")
I downloaded new classifiers from Silva 144 version. I used qiime2-amplicon-2025.10 because I wanted to see how much different the results were from a previous run when I got intoo a sequence of issues as soon as I start… --- ## [Dada2: Trimming 4 pe sequencing runs so they can merge (3 runs 150 pb pe, 1 run 100 pb pe)](https://forum.qiime2.org/t/dada2-trimming-4-pe-sequencing-runs-so-they-can-merge-3-runs-150-pb-pe-1-run-100-pb-pe/34322)
**Author:** [@baenal](https://forum.qiime2.org/u/baenal)\ **Replies:** 2\ **Last updated:** [September 11, 2026, 2:18pm UTC](https://forum.qiime2.org/t/dada2-trimming-4-pe-sequencing-runs-so-they-can-merge-3-runs-150-pb-pe-1-run-100-pb-pe/34322 "2026-09-11T14:18:12Z")
Hi all, I have found bits and pieces of my question answered across different discussions, but nothing that completes the picture. I have 4 different sequencing runs that I would like to merge later on. These are from d… --- ## [SILVA 138 and 144 classifiers are now available for QIIME 2 2026.7](https://forum.qiime2.org/t/silva-138-and-144-classifiers-are-now-available-for-qiime-2-2026-7/34321)
**Author:** [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Replies:** 0\ **Last updated:** [September 10, 2026, 1:37pm UTC](https://forum.qiime2.org/t/silva-138-and-144-classifiers-are-now-available-for-qiime-2-2026-7/34321 "2026-09-10T13:37:52Z")
Hi all, Silva classifiers are now available for SILVA 138.2 and 144 on SILVA's QIIME 2 classifiers page: Thanks @silva-team for preparing these! --- ## [PacBio ITS workflow - some questions](https://forum.qiime2.org/t/pacbio-its-workflow-some-questions/34263)
**Author:** [@Rob\_DNA](https://forum.qiime2.org/u/Rob_DNA)\ **Replies:** 4\ **Last updated:** [September 9, 2026, 9:41am UTC](https://forum.qiime2.org/t/pacbio-its-workflow-some-questions/34263 "2026-09-09T09:41:44Z")
Hello, I've use QIIME2 quite a lot for Illumina paired end data, but now it is the first time I'll use it with PacBio full ITS data. The primers used are ITS9mun (GTACACACCGCCCGTCG) and ITS4ngsUni (CGCCTSCSCTTANTDATATGC… --- ## [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… --- ## [Handling paired before/after microbiome data](https://forum.qiime2.org/t/handling-paired-before-after-microbiome-data/34242)
**Author:** [@kbenmd](https://forum.qiime2.org/u/kbenmd)\ **Replies:** 4\ **Last updated:** [September 8, 2026, 2:03am UTC](https://forum.qiime2.org/t/handling-paired-before-after-microbiome-data/34242 "2026-09-08T02:03:56Z")
Hi everyone, I am working on analyzing the microbiome of a specific human body site to compare patients before and after a clinical intervention. Because the data is collected from the exact same patients at two differe… --- ## [add DartUniFrac](https://forum.qiime2.org/t/add-dartunifrac/34312)
**Author:** [@jianshu93](https://forum.qiime2.org/u/jianshu93)\ **Replies:** 3\ **Last updated:** [September 7, 2026, 9:15am UTC](https://forum.qiime2.org/t/add-dartunifrac/34312 "2026-09-07T09:15:29Z")
Dear Qiime 2 team, We published DartUniFrac recently ( Megascale microbiome analysis with DartUniFrac | Nature Biotechnology ) and wonder if you can also add support for it. It is available as a bioconda binary already.… --- ## [Scheduled Forum Maintenance: 5-6 Sept 2026](https://forum.qiime2.org/t/scheduled-forum-maintenance-5-6-sept-2026/34314)
**Author:** [@q2d2](https://forum.qiime2.org/u/q2d2)\ **Replies:** 0\ **Last updated:** [September 4, 2026, 4:37pm UTC](https://forum.qiime2.org/t/scheduled-forum-maintenance-5-6-sept-2026/34314 "2026-09-04T16:37:57Z")
Hi all, We will be doing some maintenance on the forum tomorrow, September 5th 2025 around 12pm CET (central european time). We expect this to take a few hours (without running into any unforseen snags) and will be plac… --- ## [FUNGuild: Best practice for OTUs with multiple guilds (no primary “|”), and handling “Plant Pathogen” priority?](https://forum.qiime2.org/t/funguild-best-practice-for-otus-with-multiple-guilds-no-primary-and-handling-plant-pathogen-priority/33595)
**Author:** [@Salma\_Sarker](https://forum.qiime2.org/u/Salma_Sarker)\ **Replies:** 3\ **Last updated:** [September 4, 2026, 6:47am UTC](https://forum.qiime2.org/t/funguild-best-practice-for-otus-with-multiple-guilds-no-primary-and-handling-plant-pathogen-priority/33595 "2026-09-04T06:47:09Z")
Hi all, I’m working with fungal OTUs/ASVs (ITS) from a QIIME 2 workflow and assigning functional guilds with FUNGuild. I’ve been stuck on how to handle multiple guild assignments, and I’d really appreciate guidance or re… --- ## [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… --- ## [.biom to .tsv is losing per-sample data from FeatureTable\[Frequency\]](https://forum.qiime2.org/t/biom-to-tsv-is-losing-per-sample-data-from-featuretable-frequency/34311)
**Author:** [@Emma\_Gardner](https://forum.qiime2.org/u/Emma_Gardner)\ **Replies:** 1\ **Last updated:** [September 3, 2026, 1:25pm UTC](https://forum.qiime2.org/t/biom-to-tsv-is-losing-per-sample-data-from-featuretable-frequency/34311 "2026-09-03T13:25:22Z")
.biom to .tsv is losing per-sample data from FeatureTable\[Frequency\] Hi! I'm trying to export my .qza files so that I can use some other analysis tools in R, and for some reason, it looks like I'm losing my per-sample fr… --- ## [Retrieving FASTQ files after PRONAME filtering for quality control](https://forum.qiime2.org/t/retrieving-fastq-files-after-proname-filtering-for-quality-control/34298)
**Author:** [@zahir](https://forum.qiime2.org/u/zahir)\ **Replies:** 3\ **Last updated:** [September 3, 2026, 9:50am UTC](https://forum.qiime2.org/t/retrieving-fastq-files-after-proname-filtering-for-quality-control/34298 "2026-09-03T09:50:33Z")
Hello everyone, I am currently using PRONAME to analyse full-length 16S rRNA Nanopore sequencing data. I used the gzipped FASTQ (.fastq.gz) files directly from MinKNOW as the input for PRONAME and followed the tutorial… --- ## [kmers for taxonomy-free beta-diversity measures: an opportunity to integrate amplicon and shotgun analysis?](https://forum.qiime2.org/t/kmers-for-taxonomy-free-beta-diversity-measures-an-opportunity-to-integrate-amplicon-and-shotgun-analysis/34309)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 2\ **Last updated:** [September 2, 2026, 4:47pm UTC](https://forum.qiime2.org/t/kmers-for-taxonomy-free-beta-diversity-measures-an-opportunity-to-integrate-amplicon-and-shotgun-analysis/34309 "2026-09-02T16:47:12Z")
Greetings Qiime-izens, :qiime2::popcorn: TL;DR below. :stopwatch: I have some environmental megagenomic samples that have been analyzed with 16S and shotgun sequencing. So, we ideally want our beta diversity measures t… --- ## [AVITI vs. Illumina](https://forum.qiime2.org/t/aviti-vs-illumina/34303)
**Author:** [@szec](https://forum.qiime2.org/u/szec)\ **Replies:** 3\ **Last updated:** [September 1, 2026, 5:59pm UTC](https://forum.qiime2.org/t/aviti-vs-illumina/34303 "2026-09-01T17:59:47Z")
Hi all, I have 3 years of data; the first (2023) was sequenced using Illumina and the last two (2024 & 2025) were sequenced using AVITI. When processing them, everything runs smoothly, but when I try to combine them, th… --- ## [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 … [Next page](https://forum.qiime2.org/latest.md?page=1)