# \#metagenomics **URL:** https://forum.qiime2.org/tag/metagenomics/249.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Functional annotation using Greengenes2](https://forum.qiime2.org/t/functional-annotation-using-greengenes2/34218)
**Author:** [@emnatasha](https://forum.qiime2.org/u/emnatasha)\ **Replies:** 5\ **Last updated:** [July 2, 2026, 9:19pm UTC](https://forum.qiime2.org/t/functional-annotation-using-greengenes2/34218 "2026-07-02T21:19:41Z")
Hi QIIME2 developers, contributors, and moderators, Thank you very much for actively maintaining the infrastructure of QIIME2 and moderating the QIIME2 forum. I am processing my shotgun metagenomic sequencing reads usin… --- ## [Alpha and Beta Diversity analysis using shotgun metagenomics data](https://forum.qiime2.org/t/alpha-and-beta-diversity-analysis-using-shotgun-metagenomics-data/33930)
**Author:** [@Synapse](https://forum.qiime2.org/u/Synapse)\ **Replies:** 2\ **Last updated:** [January 26, 2026, 7:48am UTC](https://forum.qiime2.org/t/alpha-and-beta-diversity-analysis-using-shotgun-metagenomics-data/33930 "2026-01-26T07:48:06Z")
Dear all, Good day QIIME community! I am new to QIIME2 and would appreciate some guidance. We are working on a project involving a biofilm, and we plan to send our samples to a facility for shotgun metagenomic sequenci… --- ## [Comparing 16S and shotgun metagenomic data with greengenes2](https://forum.qiime2.org/t/comparing-16s-and-shotgun-metagenomic-data-with-greengenes2/33895)
**Author:** [@Bark9299](https://forum.qiime2.org/u/Bark9299)\ **Replies:** 3\ **Last updated:** [January 20, 2026, 9:51pm UTC](https://forum.qiime2.org/t/comparing-16s-and-shotgun-metagenomic-data-with-greengenes2/33895 "2026-01-20T21:51:58Z")
Hello, I have both 16S rRNA V4 and shotgun metagenomic data from the same samples and I want to broadly compare overall patterns in alpha and beta diversity by treatment, and in seeing whether 16S and shotgun data recov… --- ## [How can I import an existing Bracken database into QIIME2?](https://forum.qiime2.org/t/how-can-i-import-an-existing-bracken-database-into-qiime2/33801)
**Author:** [@ehdud0505](https://forum.qiime2.org/u/ehdud0505)\ **Replies:** 2\ **Last updated:** [November 20, 2025, 2:12am UTC](https://forum.qiime2.org/t/how-can-i-import-an-existing-bracken-database-into-qiime2/33801 "2025-11-20T02:12:03Z")
Dear qiime2 teams, Hi everyone, My professor has already installed a Kraken2 database on our server, so I am trying to use the existing database instead of building a new one with kraken2-build provided by the QIIME2 m… --- ## [online course - Environmental Metagenomics -13-17 October](https://forum.qiime2.org/t/online-course-environmental-metagenomics-13-17-october/33688)
**Author:** [@Physalia-courses](https://forum.qiime2.org/u/Physalia-courses)\ **Replies:** 0\ **Last updated:** [September 30, 2025, 6:59pm UTC](https://forum.qiime2.org/t/online-course-environmental-metagenomics-13-17-october/33688 "2025-09-30T18:59:48Z")
Dear all, there are only a few seats remaining for the Physalia online course on Environmental Metagenomics! Dates: 13-17 October (9 am -1 PM Berlin time) Course website: https://www.physalia-courses.org/courses-works… --- ## [Issue with Taxonomy Assignment Using Kraken and Custom Database (BOLD, Nemabiome) in QIIME2](https://forum.qiime2.org/t/issue-with-taxonomy-assignment-using-kraken-and-custom-database-bold-nemabiome-in-qiime2/32476)
**Author:** [@SingeunOh](https://forum.qiime2.org/u/SingeunOh)\ **Replies:** 4\ **Last updated:** [February 14, 2025, 4:22pm UTC](https://forum.qiime2.org/t/issue-with-taxonomy-assignment-using-kraken-and-custom-database-bold-nemabiome-in-qiime2/32476 "2025-02-14T16:22:30Z")
Hello everyone, I’m currently using Kraken2 for taxonomy assignment of shotgun metagenomic sequences within QIIME2. However, I’ve encountered strange results when comparing Kraken’s assignments to those obtained from N… --- ## [Running simulated reads through DADA2](https://forum.qiime2.org/t/running-simulated-reads-through-dada2/30923)
**Author:** [@cberta11](https://forum.qiime2.org/u/cberta11)\ **Replies:** 1\ **Last updated:** [July 24, 2024, 5:10pm UTC](https://forum.qiime2.org/t/running-simulated-reads-through-dada2/30923 "2024-07-24T17:10:43Z")
Good afternoon, I am trying to run simulated reads through the QIIME2 pipeline and am having issues denoising them with DADA2. The reads were created with CAMISIM (using only rRNA gene nucleotide sequences as the input … --- ## [Qiime2 metagenome distribution on Google colab](https://forum.qiime2.org/t/qiime2-metagenome-distribution-on-google-colab/30739)
**Author:** [@Joel\_Daniel\_Tigrero](https://forum.qiime2.org/u/Joel_Daniel_Tigrero)\ **Replies:** 3\ **Last updated:** [July 8, 2024, 5:18pm UTC](https://forum.qiime2.org/t/qiime2-metagenome-distribution-on-google-colab/30739 "2024-07-08T17:18:15Z")
Hello Qiime2 community! I want to use the qiime2 metagenome distribution on google colab. Is this feasible? So far, i have only found a tutorial on setting up and utilizing the qiime2 amplicon distribution on google co… --- ## [qiime2-metagenome-2024.5 feature-classifier](https://forum.qiime2.org/t/qiime2-metagenome-2024-5-feature-classifier/30678)
**Author:** [@Anita\_Chand](https://forum.qiime2.org/u/Anita_Chand)\ **Replies:** 5\ **Last updated:** [July 2, 2024, 2:04pm UTC](https://forum.qiime2.org/t/qiime2-metagenome-2024-5-feature-classifier/30678 "2024-07-02T14:04:32Z")
Hi everyone, I am trying to train classifier with ref sequence file and taxonomy file but the command ending with the message 'killed'. qiime tools import --type FeatureData\[Sequence\] --input-path ref\_seq.fa --ou… --- ## [import files from qiime2 into q2-woltka](https://forum.qiime2.org/t/import-files-from-qiime2-into-q2-woltka/30395)
**Author:** [@turtle](https://forum.qiime2.org/u/turtle)\ **Replies:** 0\ **Last updated:** [June 5, 2024, 5:09am UTC](https://forum.qiime2.org/t/import-files-from-qiime2-into-q2-woltka/30395 "2024-06-05T05:09:14Z")
I've been trying to use q2-woltka to analyze whole genome shotgun sequence data. I've downloaded the sequence data with the help of the q2-fondue plugin. So now what I have is the following files, The problem is q2-… --- ## [Is it possible to check a specific gene level in a specific genus?](https://forum.qiime2.org/t/is-it-possible-to-check-a-specific-gene-level-in-a-specific-genus/28963)
**Author:** [@sooni](https://forum.qiime2.org/u/sooni)\ **Replies:** 7\ **Last updated:** [January 25, 2024, 5:43pm UTC](https://forum.qiime2.org/t/is-it-possible-to-check-a-specific-gene-level-in-a-specific-genus/28963 "2024-01-25T17:43:29Z")
Hello. I always thanks for your help. I want to check a specific gene level in a specific genus. Is it possible with QIIME2-Shotgun distribution? If possible, how can I do it? I'm sorry if this may be a topic that ov… --- ## [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… --- ## [Large metagenomic dataset](https://forum.qiime2.org/t/large-metagenomic-dataset/28516)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 5\ **Last updated:** [December 7, 2023, 8:43am UTC](https://forum.qiime2.org/t/large-metagenomic-dataset/28516 "2023-12-07T08:43:10Z")
Dear Qiimers! I am happy to play with a large metagenomic dataset (\> 400 samples). I am facing some difficulties running it, mostly due to the large size of imported reads (1.6 TB). Am I safe to assume that splitting t… --- ## [Regarding Databases](https://forum.qiime2.org/t/regarding-databases/27285)
**Author:** [@Jaykishan\_Solanki](https://forum.qiime2.org/u/Jaykishan_Solanki)\ **Replies:** 3\ **Last updated:** [August 3, 2023, 5:32pm UTC](https://forum.qiime2.org/t/regarding-databases/27285 "2023-08-03T17:32:15Z")
can anyone guide me from where i can get pre-formatted databases for ready to run 18s rRNA data analysis ?? --- ## [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…