# Community Contributions **URL:** https://forum.qiime2.org/c/community-contributions/15.md?page=1 [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) **Page:** 2 --- ## [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… --- ## [eKOI database in qiime2 format](https://forum.qiime2.org/t/ekoi-database-in-qiime2-format/32145)
**Author:** [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)\ **Replies:** 0\ **Last updated:** [December 17, 2024, 8:20am UTC](https://forum.qiime2.org/t/ekoi-database-in-qiime2-format/32145 "2024-12-17T08:20:14Z")
I've been having some issues with assigning taxonomy to some COI data so when I saw the eKOI preprint I rushed to convert it to be useable in qiime2. It didn't solve my issues but thought I'd share in case anyone wanted … --- ## [Python 3 function cld4py to assign compact letter display letters](https://forum.qiime2.org/t/python-3-function-cld4py-to-assign-compact-letter-display-letters/31951)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 1\ **Last updated:** [December 7, 2024, 8:54pm UTC](https://forum.qiime2.org/t/python-3-function-cld4py-to-assign-compact-letter-display-letters/31951 "2024-12-07T20:54:01Z")
Dear all, For a while I was unsuccessfully looking for Python3 package to assign Compact Letter Display letters based on the contrasts after pairwise comparisons. Then, I decided to write a function that will do the jo… --- ## [Pretrained EUKARYOME(v1.9) Database for Eukaryotic Taxonomy in QIIME2](https://forum.qiime2.org/t/pretrained-eukaryome-v1-9-database-for-eukaryotic-taxonomy-in-qiime2/31479)
**Author:** [@soyeon\_kim](https://forum.qiime2.org/u/soyeon_kim)\ **Replies:** 4\ **Last updated:** [November 22, 2024, 10:16am UTC](https://forum.qiime2.org/t/pretrained-eukaryome-v1-9-database-for-eukaryotic-taxonomy-in-qiime2/31479 "2024-11-22T10:16:17Z")
Hello, QIIME2 users. I have recently trained the newly released EUKARYOME database in QIIME2 format. More information can be found on the official website (https://eukaryome.org/). The EUKARYOME database integrates oth… --- ## [Curated 16S database (MIMt)](https://forum.qiime2.org/t/curated-16s-database-mimt/31873)
**Author:** [@A\_Munoz](https://forum.qiime2.org/u/A_Munoz)\ **Replies:** 2\ **Last updated:** [November 15, 2024, 3:19pm UTC](https://forum.qiime2.org/t/curated-16s-database-mimt/31873 "2024-11-15T15:19:59Z")
I would like to announce to the QIIME community the launch of a new 16S database for taxonomic assignment compatible with QIIME. MIMt is composed of 16S sequences from species well identified and curated from RefSeq. Al… --- ## [Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank](https://forum.qiime2.org/t/using-rescript-to-compile-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947)
**Author:** [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Replies:** 0\ **Last updated:** [August 4, 2020, 3:38pm UTC](https://forum.qiime2.org/t/using-rescript-to-compile-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947 "2020-08-04T15:38:16Z")
This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequenc… --- ## [add Linear Regression Lines to Mantel Test](https://forum.qiime2.org/t/add-linear-regression-lines-to-mantel-test/31494)
**Author:** [@CarlyRae](https://forum.qiime2.org/u/CarlyRae)\ **Replies:** 1\ **Last updated:** [September 24, 2024, 7:35pm UTC](https://forum.qiime2.org/t/add-linear-regression-lines-to-mantel-test/31494 "2024-09-24T19:35:38Z")
Response to: Is there a way to add Linear Regression Lines to Mantel Test? I had to do some searching around and thinking about this and figured out the code and wanted to share. Code is in R. library(phyloseq) data(Gl… --- ## [Fungal ITS analysis tutorial](https://forum.qiime2.org/t/fungal-its-analysis-tutorial/7351)
**Author:** [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Replies:** 15\ **Last updated:** [May 21, 2024, 12:09pm UTC](https://forum.qiime2.org/t/fungal-its-analysis-tutorial/7351 "2024-05-21T12:09:41Z")
Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as… --- ## [Available: Pre-trained classifier of V3-V4 (341F, 805R) region with gg\_99](https://forum.qiime2.org/t/available-pre-trained-classifier-of-v3-v4-341f-805r-region-with-gg-99/3275)
**Author:** [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)\ **Replies:** 6\ **Last updated:** [May 17, 2024, 8:34pm UTC](https://forum.qiime2.org/t/available-pre-trained-classifier-of-v3-v4-341f-805r-region-with-gg-99/3275 "2024-05-17T20:34:41Z")
Hi folks, In case anyone is interested I have a pretrained classifier on the V3-V4 region using the following primers: 341F: CCTACGGGNGGCWGCAG 805R: GACTACHVGGGTATCTAATCC The primer set is taken from Illumina's 16S l… --- ## [Importing dada2 and Phyloseq objects to QIIME 2](https://forum.qiime2.org/t/importing-dada2-and-phyloseq-objects-to-qiime-2/4683)
**Author:** [@ChristianEdwardson](https://forum.qiime2.org/u/ChristianEdwardson)\ **Replies:** 7\ **Last updated:** [May 14, 2024, 11:55pm UTC](https://forum.qiime2.org/t/importing-dada2-and-phyloseq-objects-to-qiime-2/4683 "2024-05-14T23:55:22Z")
Importing dada2 and/or Phyloseq objects to QIIME 2 Background This tutorial describes how to take feature/OTU tables, taxonomy tables, and sample data (metadata) from R and import into QIIME 2. This might be useful if yo… --- ## [draft tutorial for shotgun metagenomics with QIIME 2](https://forum.qiime2.org/t/draft-tutorial-for-shotgun-metagenomics-with-qiime-2/28040)
**Author:** [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Replies:** 6\ **Last updated:** [October 31, 2023, 1:10pm UTC](https://forum.qiime2.org/t/draft-tutorial-for-shotgun-metagenomics-with-qiime-2/28040 "2023-10-31T13:10:29Z")
Update: We now have an updated tutorial on performing shotgun metagenomic data analysis using MOSHPIT (which we formerly referred to as the QIIME 2 Shotgun Metagenomics Distribution). You can find that on ReadTheDocs at: … --- ## [Q2-ghost-tree Plugin: Community Tutorial for Creating Hybrid-Gene Phylogenetic Trees](https://forum.qiime2.org/t/q2-ghost-tree-plugin-community-tutorial-for-creating-hybrid-gene-phylogenetic-trees/6139)
**Author:** [@Jennifer\_Fouquier](https://forum.qiime2.org/u/Jennifer_Fouquier)\ **Replies:** 3\ **Last updated:** [April 24, 2024, 11:46am UTC](https://forum.qiime2.org/t/q2-ghost-tree-plugin-community-tutorial-for-creating-hybrid-gene-phylogenetic-trees/6139 "2024-04-24T11:46:31Z")
q2-ghost-tree is a plugin for creating hybrid trees within the QIIME 2 environment This tutorial is also hosted as a README for the plugin GitHub - JTFouquier/q2-ghost-tree: QIIME 2 Plugin Development ghost-tree is a bi… --- ## [Recommendations for installing older versions of QIIME 2](https://forum.qiime2.org/t/recommendations-for-installing-older-versions-of-qiime-2/28956)
**Author:** [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Replies:** 0\ **Last updated:** [January 18, 2024, 10:18pm UTC](https://forum.qiime2.org/t/recommendations-for-installing-older-versions-of-qiime-2/28956 "2024-01-18T22:18:31Z")
While we recommend keeping your version of QIIME 2 up to date, we recognize that QIIME 2 users sometimes may wish to install older versions of QIIME 2 - whether that be to test/replicate behavior that existed within a pa… --- ## [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-amr: A Plugin for Antibiotic Resistance Gene Analysis in Qiime2](https://forum.qiime2.org/t/q2-amr-a-plugin-for-antibiotic-resistance-gene-analysis-in-qiime2/29007)
**Author:** [@Vinzent\_Risch](https://forum.qiime2.org/u/Vinzent_Risch)\ **Replies:** 0\ **Last updated:** [January 23, 2024, 4:29pm UTC](https://forum.qiime2.org/t/q2-amr-a-plugin-for-antibiotic-resistance-gene-analysis-in-qiime2/29007 "2024-01-23T16:29:18Z")
Hello Qiime2 Community! I'm excited to introduce q2-amr, a new Qiime2 plugin, designed to integrate Antibiotic Resistance Gene (ARG) analysis into Qiime2. This plugin leverages the Resistance Gene Identifier (RGI) and t… --- ## [Building a COI database from NCBI references](https://forum.qiime2.org/t/building-a-coi-database-from-ncbi-references/16500)
**Author:** [@devonorourke](https://forum.qiime2.org/u/devonorourke)\ **Replies:** 2\ **Last updated:** [November 19, 2020, 1:35pm UTC](https://forum.qiime2.org/t/building-a-coi-database-from-ncbi-references/16500 "2020-11-19T13:35:27Z")
:construction: :stop\_sign::construction: :stop\_sign::construction: :stop\_sign::construction: :stop\_sign::construction: :stop\_sign: Citation: If you use the following COI resources or RESCRIPt for COI database preparatio… --- ## [Evident: Effect size and power calculations for microbiome community data](https://forum.qiime2.org/t/evident-effect-size-and-power-calculations-for-microbiome-community-data/23146)
**Author:** [@gibsramen](https://forum.qiime2.org/u/gibsramen)\ **Replies:** 9\ **Last updated:** [December 19, 2023, 4:08am UTC](https://forum.qiime2.org/t/evident-effect-size-and-power-calculations-for-microbiome-community-data/23146 "2023-12-19T04:08:32Z")
Evident: Community Tutorial Evident is a tool for calculating the effect sizes of sample groupings microbiome data and performing statistical power analysis. With Evident, you can easily explore columns in your metadata … --- ## [Querying for public microbiome data in Qiita using redbiom](https://forum.qiime2.org/t/querying-for-public-microbiome-data-in-qiita-using-redbiom/4653)
**Author:** [@wasade](https://forum.qiime2.org/u/wasade)\ **Replies:** 14\ **Last updated:** [December 14, 2023, 4:28pm UTC](https://forum.qiime2.org/t/querying-for-public-microbiome-data-in-qiita-using-redbiom/4653 "2023-12-14T16:28:08Z")
redbiom (canonically pronounced "red biome") is a caching layer that facilitates the rapid retrieval of existing processed microbiome datasets. It allows for querying presence of exact sequence variants, retrieval of sam… --- ## [Importing Kraken2 and bracken databases into qiime2!](https://forum.qiime2.org/t/importing-kraken2-and-bracken-databases-into-qiime2/28384)
**Author:** [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)\ **Replies:** 0\ **Last updated:** [November 22, 2023, 11:24am UTC](https://forum.qiime2.org/t/importing-kraken2-and-bracken-databases-into-qiime2/28384 "2023-11-22T11:24:18Z")
Hello all, With the release of Qiime2-shotgun and shotgun metagenomics tutorial. I'm just giving a quick writeup/tutorial on how to import precompiled kraken2 and bracken databases. The first step is to download the ap… --- ## [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… --- ## [Moving Pictures Python API tutorial (QIIME2 2018.4)](https://forum.qiime2.org/t/moving-pictures-python-api-tutorial-qiime2-2018-4/4112)
**Author:** [@tomasz](https://forum.qiime2.org/u/tomasz)\ **Replies:** 0\ **Last updated:** [May 10, 2018, 9:46pm UTC](https://forum.qiime2.org/t/moving-pictures-python-api-tutorial-qiime2-2018-4/4112 "2018-05-10T21:46:51Z")
I rewrote the "Moving Pictures" tutorial using QIIME2 Python API. The original QIIME2 CLI "Moving Pictures" tutorial can be accessed here. It takes advantage of the latest QIIME2 2018.4 functionalities, especially displ… --- ## [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… --- ## [q2-krona: Plugin for creating Krona plots](https://forum.qiime2.org/t/q2-krona-plugin-for-creating-krona-plots/21294)
**Author:** [@the\_dummy](https://forum.qiime2.org/u/the_dummy)\ **Replies:** 27\ **Last updated:** [May 26, 2023, 8:15am UTC](https://forum.qiime2.org/t/q2-krona-plugin-for-creating-krona-plots/21294 "2023-05-26T08:15:55Z")
Hello everyone, I've finally got time from work and finished the plugin. :tada: Special thanks to @Nicholas\_Bokulich for suggesting making my own plugin, and @thermokarst for revision. The plugin is available at my gi… --- ## [q2-SCRuB release](https://forum.qiime2.org/t/q2-scrub-release/26609)
**Author:** [@George\_Austin](https://forum.qiime2.org/u/George_Austin)\ **Replies:** 0\ **Last updated:** [May 26, 2023, 3:51am UTC](https://forum.qiime2.org/t/q2-scrub-release/26609 "2023-05-26T03:51:24Z")
We are proud to (belatedly) announce the release of the q2-SCRuB plugin! SCRuB is a tool designed to help researchers address the common issue of contamination in microbial studies. Principal concept SCRuB is a proba… --- ## [webapp to run analysis pipeline (italian language)](https://forum.qiime2.org/t/webapp-to-run-analysis-pipeline-italian-language/26137)
**Author:** [@cami3](https://forum.qiime2.org/u/cami3)\ **Replies:** 8\ **Last updated:** [May 12, 2023, 10:11pm UTC](https://forum.qiime2.org/t/webapp-to-run-analysis-pipeline-italian-language/26137 "2023-05-12T22:11:13Z")
Hello everybody, to anyone interested I recently developed a webapp using the streamlit python library, that allows users to run an analysis pipeline based on this great package qiime2, in a user-friendly manner, with in… --- ## [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… --- ## [Working with plants? Try "PLANiTS": a plant ITS reference database for QIIME2](https://forum.qiime2.org/t/working-with-plants-try-planits-a-plant-its-reference-database-for-qiime2/15586)
**Author:** [@ElisaBanchi](https://forum.qiime2.org/u/ElisaBanchi)\ **Replies:** 6\ **Last updated:** [April 3, 2023, 7:56pm UTC](https://forum.qiime2.org/t/working-with-plants-try-planits-a-plant-its-reference-database-for-qiime2/15586 "2023-04-03T19:56:41Z")
Hello QIIME2 users! I am Elisa Banchi, a Research Fellow at the National Institute of Oceanography of Trieste, Italy. With the University of Trieste, we have developed PLANiTS, a reference dataset for plant ITS formatt… --- ## [Importing sequence data with lower-case nucleotide characters. Constructing an RDP classifier as an example.](https://forum.qiime2.org/t/importing-sequence-data-with-lower-case-nucleotide-characters-constructing-an-rdp-classifier-as-an-example/25158)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 0\ **Last updated:** [January 6, 2023, 6:42pm UTC](https://forum.qiime2.org/t/importing-sequence-data-with-lower-case-nucleotide-characters-constructing-an-rdp-classifier-as-an-example/25158 "2023-01-06T18:42:48Z")
Using qiime2-2022.11 or later, we can now import DNA and RNA sequence files that contain lower-case sequence characters. Upon import, these nucleotide bases will be converted to the standard upper-case IUPAC format, usin… --- ## [q2-mOTUs beta release 🎉](https://forum.qiime2.org/t/q2-motus-beta-release/25296)
**Author:** [@crusher083](https://forum.qiime2.org/u/crusher083)\ **Replies:** 3\ **Last updated:** [March 22, 2023, 1:17pm UTC](https://forum.qiime2.org/t/q2-motus-beta-release/25296 "2023-03-22T13:17:48Z")
We are proud to announce beta release of the q2-mOTUs plugin :tada: :tada: :tada: mOTU is a tool for taxonomical profiling of metagenomic data extensively validated during CAMI Challenge. Principal concept mOTU is an a… --- ## [q2-repeat-rarefy: QIIME2 plugin for generating the average rarefied table for library size normalization using repeated rarefaction](https://forum.qiime2.org/t/q2-repeat-rarefy-qiime2-plugin-for-generating-the-average-rarefied-table-for-library-size-normalization-using-repeated-rarefaction/18032)
**Author:** [@yxia](https://forum.qiime2.org/u/yxia)\ **Replies:** 1\ **Last updated:** [March 22, 2023, 11:50am UTC](https://forum.qiime2.org/t/q2-repeat-rarefy-qiime2-plugin-for-generating-the-average-rarefied-table-for-library-size-normalization-using-repeated-rarefaction/18032 "2023-03-22T11:50:16Z")
q2-repeat-rarefy: QIIME2 plugin for generating the average rarefied table for library size normalization using repeated rarefaction When handling a sparse dataset, I noticed that the rare taxa were easily ignored by the… [Previous page](https://forum.qiime2.org/c/community-contributions/15.md) [Next page](https://forum.qiime2.org/c/community-contributions/15.md?page=2)