# \#greengenes **URL:** https://forum.qiime2.org/tag/greengenes/59.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Difficulty assigning taxonomy to cyanobacterial ASVs](https://forum.qiime2.org/t/difficulty-assigning-taxonomy-to-cyanobacterial-asvs/33226)
**Author:** [@Mahima\_y](https://forum.qiime2.org/u/Mahima_y)\ **Replies:** 2\ **Last updated:** [June 5, 2025, 5:48pm UTC](https://forum.qiime2.org/t/difficulty-assigning-taxonomy-to-cyanobacterial-asvs/33226 "2025-06-05T17:48:24Z")
Hello! I am trying to find the best method and database to assign taxonomy to my 1,107 ASVs. (For context, my samples were collected from seawater that was filtered and prepared for sequencing, bioinformatics, etc). Beca… --- ## [Comparison of OTU Identifications with Silva 138.1 and Greengenes 2022.10 databases](https://forum.qiime2.org/t/comparison-of-otu-identifications-with-silva-138-1-and-greengenes-2022-10-databases/32740)
**Author:** [@Bonita\_Mc](https://forum.qiime2.org/u/Bonita_Mc)\ **Replies:** 7\ **Last updated:** [March 16, 2025, 2:57pm UTC](https://forum.qiime2.org/t/comparison-of-otu-identifications-with-silva-138-1-and-greengenes-2022-10-databases/32740 "2025-03-16T14:57:47Z")
I have been using the bioinformatics services provided by Novogene. We use the most cost efficient option which still uses QIIME and the Silva 138.1 database. I have made my own classifier using the Greengenes 2022.10 b… --- ## [Introducing Greengenes2 2022.10](https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291)
**Author:** [@wasade](https://forum.qiime2.org/u/wasade)\ **Replies:** 71\ **Last updated:** [October 11, 2024, 10:01pm UTC](https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291 "2024-10-11T22:01:51Z")
IMPORTANT: Greengenes2 2022.10 has been replaced with 2024.09. More information can be found here. The commands and examples noted within this tutorial remain relevant though. Introduction We are excited to announce a n… --- ## [gg-13-8-99-515-806-nb-classifier.qza is not up-to-date](https://forum.qiime2.org/t/gg-13-8-99-515-806-nb-classifier-qza-is-not-up-to-date/32104)
**Author:** [@kevnael](https://forum.qiime2.org/u/kevnael)\ **Replies:** 8\ **Last updated:** [December 13, 2024, 9:44am UTC](https://forum.qiime2.org/t/gg-13-8-99-515-806-nb-classifier-qza-is-not-up-to-date/32104 "2024-12-13T09:44:38Z")
Hello, I hope you are doing well. I have been able to analyse my data but I noticed that at the genus level, I have "UNCLASSIFIED CLOSTRIDIACEAE" which is a family name. I suspect that the classifier I used (gg-13-8-99… --- ## [Best Discussion Forum for Greengenes 2?](https://forum.qiime2.org/t/best-discussion-forum-for-greengenes-2/30849)
**Author:** [@pone](https://forum.qiime2.org/u/pone)\ **Replies:** 7\ **Last updated:** [August 28, 2024, 11:25pm UTC](https://forum.qiime2.org/t/best-discussion-forum-for-greengenes-2/30849 "2024-08-28T23:25:49Z")
Where is the best discussion forum for the GreenGenes 2 bioinformatics database? I tried to run a sample through GreenGenes 2, because I heard it has more accurate genera classification. Unfortunately, it also has lo… --- ## [Database With Best Accuracy at Genus Level for Human Microbiome?](https://forum.qiime2.org/t/database-with-best-accuracy-at-genus-level-for-human-microbiome/31188)
**Author:** [@pone](https://forum.qiime2.org/u/pone)\ **Replies:** 8\ **Last updated:** [August 28, 2024, 7:01pm UTC](https://forum.qiime2.org/t/database-with-best-accuracy-at-genus-level-for-human-microbiome/31188 "2024-08-28T19:01:37Z")
If you have an Illumina FASTQ corresponding to a human stool sample, which genomics databases and bioinformatics pathway(s) will give you the best accuracy at the genus level? Is there any research that ranks the datab… --- ## [Reconciling 16s Databases in a Single Pipeline](https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258)
**Author:** [@pone](https://forum.qiime2.org/u/pone)\ **Replies:** 5\ **Last updated:** [August 28, 2024, 3:36pm UTC](https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258 "2024-08-28T15:36:18Z")
Is it possible to create a pipeline for 16s sequences that would try to reconcile sequence assignments across multiple databases? The point of this is to expose ambiguities and different assignments explicitly within … --- ## [How to train the classifier for V3-V4 region with 99% identity using full length seuqnces from new relase of GreenGenes-2022??](https://forum.qiime2.org/t/how-to-train-the-classifier-for-v3-v4-region-with-99-identity-using-full-length-seuqnces-from-new-relase-of-greengenes-2022/27991)
**Author:** [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)\ **Replies:** 9\ **Last updated:** [June 20, 2024, 7:20pm UTC](https://forum.qiime2.org/t/how-to-train-the-classifier-for-v3-v4-region-with-99-identity-using-full-length-seuqnces-from-new-relase-of-greengenes-2022/27991 "2024-06-20T19:20:57Z")
Hello All, I want to perform functional annotation using Picrust2 plugin. Blockquote First of all I want to train my classifier for V3-V4 region with 99% identity for latest release of greengenes-2022 Blockquote. … --- ## [train a greengenes 2022 classifier for forward reads only](https://forum.qiime2.org/t/train-a-greengenes-2022-classifier-for-forward-reads-only/28508)
**Author:** [@mawa86](https://forum.qiime2.org/u/mawa86)\ **Replies:** 4\ **Last updated:** [December 7, 2023, 2:17pm UTC](https://forum.qiime2.org/t/train-a-greengenes-2022-classifier-for-forward-reads-only/28508 "2023-12-07T14:17:09Z")
Hi quick question: before I train my greengenes classifier i extract the fragments i need using the same primers Ive used for my library prep pre-sequencing (V3-V4). Now my reverse reads for this particular run are of a… --- ## [issues moving between greengenes classification and diversity metrics](https://forum.qiime2.org/t/issues-moving-between-greengenes-classification-and-diversity-metrics/25972)
**Author:** [@AttilaTheBun](https://forum.qiime2.org/u/AttilaTheBun)\ **Replies:** 3\ **Last updated:** [March 30, 2023, 1:01pm UTC](https://forum.qiime2.org/t/issues-moving-between-greengenes-classification-and-diversity-metrics/25972 "2023-03-30T13:01:39Z")
Hello all! I'm having some issues with my code, and I'm using greengenes 13\_8 for my reference data, which I realize is highly supported in QIIME2 so I'm sure this is a user-end ignorance issue, but any help is appreciat… --- ## [Alternative methods to download Greengenes 16S rRNA 13\_8?](https://forum.qiime2.org/t/alternative-methods-to-download-greengenes-16s-rrna-13-8/25553)
**Author:** [@hewsy](https://forum.qiime2.org/u/hewsy)\ **Replies:** 1\ **Last updated:** [February 20, 2023, 3:24pm UTC](https://forum.qiime2.org/t/alternative-methods-to-download-greengenes-16s-rrna-13-8/25553 "2023-02-20T15:24:00Z")
Hello! I am trying to download Greengenes 16S rRNA 13\_8 from the qiime2 resource page however chrome now no longer supports FTP. Is there any alternative methods to download? I did tried something like WinSCP but still i… --- ## [Pre-trained Classifier of V3-V4 region with gg-99 (scikit-learn (0.24.1))](https://forum.qiime2.org/t/pre-trained-classifier-of-v3-v4-region-with-gg-99-scikit-learn-0-24-1/22267)
**Author:** [@Sina](https://forum.qiime2.org/u/Sina)\ **Replies:** 0\ **Last updated:** [February 23, 2022, 12:47am UTC](https://forum.qiime2.org/t/pre-trained-classifier-of-v3-v4-region-with-gg-99-scikit-learn-0-24-1/22267 "2022-02-23T00:47:13Z")
Hello, I made the V3-V4 region classifier, as was mentioned before in the forum, with these primers: 341F: CCTACGGGNGGCWGCAG 805R: GACTACHVGGGTATCTAATCC According to Illumina’s 16S library protocol (2\*300 bp). I fol… --- ## [Plugin error from diversity-lib: The table does not appear to be completely represented by the phylogeny](https://forum.qiime2.org/t/plugin-error-from-diversity-lib-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/20220)
**Author:** [@guyshur](https://forum.qiime2.org/u/guyshur)\ **Replies:** 1\ **Last updated:** [July 22, 2021, 6:30pm UTC](https://forum.qiime2.org/t/plugin-error-from-diversity-lib-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/20220 "2021-07-22T18:30:11Z")
Hello Q2 team, I am working with public OTU tables, and am trying to run some analyses. I collapsed a subset of Human Microbiome Project samples with Greengenes feature IDs with taxa collapse, and as a result I now have… --- ## [What's the difference between ;\_\_ and ;g\_\_ in Greengene database?](https://forum.qiime2.org/t/whats-the-difference-between-and-g-in-greengene-database/17615)
**Author:** [@Ryuk](https://forum.qiime2.org/u/Ryuk)\ **Replies:** 2\ **Last updated:** [December 4, 2020, 6:14am UTC](https://forum.qiime2.org/t/whats-the-difference-between-and-g-in-greengene-database/17615 "2020-12-04T06:14:16Z")
Hi everyone, When I used greengene for taxonomy classification, the results contains results as follows: k\_\_Bacteria;p\_\_Bacteroidetes;c\_\_Bacteroidia;o\_\_Bacteroidales;f\_\_\[Paraprevotellaceae\];\_\_ k\_\_Bacteria;p\_\_Bacteroid… --- ## [Resources for using classify-consensus-blast on 16S data](https://forum.qiime2.org/t/resources-for-using-classify-consensus-blast-on-16s-data/15504)
**Author:** [@emmzee](https://forum.qiime2.org/u/emmzee)\ **Replies:** 3\ **Last updated:** [July 7, 2020, 7:56pm UTC](https://forum.qiime2.org/t/resources-for-using-classify-consensus-blast-on-16s-data/15504 "2020-07-07T19:56:16Z")
Hi everyone, I've been researching the subject of assigning taxonomy -in terms of choice of database and method of classification- on Q2's forums and according to papers and official websites cited within. I am still no… --- ## [Why does Greengenes assign more features at the class and order ranks than Silva?](https://forum.qiime2.org/t/why-does-greengenes-assign-more-features-at-the-class-and-order-ranks-than-silva/8254)
**Author:** [@Fackelmann](https://forum.qiime2.org/u/Fackelmann)\ **Replies:** 8\ **Last updated:** [March 6, 2020, 3:34pm UTC](https://forum.qiime2.org/t/why-does-greengenes-assign-more-features-at-the-class-and-order-ranks-than-silva/8254 "2020-03-06T15:34:05Z")
Dear all, My questions concern the Silva and Greengenes databases to assign taxonomy in 16S rRNA gene sequencing studies. I recognize that each database has its merits and drawbacks and as such I am evaluating which of … --- ## [Greengenes Versus Silva](https://forum.qiime2.org/t/greengenes-versus-silva/13370)
**Author:** [@Tiago\_Bruno\_Rezende](https://forum.qiime2.org/u/Tiago_Bruno_Rezende)\ **Replies:** 3\ **Last updated:** [January 29, 2020, 6:14pm UTC](https://forum.qiime2.org/t/greengenes-versus-silva/13370 "2020-01-29T18:14:27Z")
Hello everyone, I know, there are at least 10 topics in the forum with the same title. I am posting this topic as the last resource to find some answers for a few doubts regarding Silva. In advance, I will disclose that… --- ## [Importing 13\_8 Greengenes database for training classifier](https://forum.qiime2.org/t/importing-13-8-greengenes-database-for-training-classifier/12097)
**Author:** [@ET1335](https://forum.qiime2.org/u/ET1335)\ **Replies:** 1\ **Last updated:** [October 22, 2019, 1:39am UTC](https://forum.qiime2.org/t/importing-13-8-greengenes-database-for-training-classifier/12097 "2019-10-22T01:39:00Z")
Hi, I have a general question about importing the 13\_8 Greengenes database into QIIME2 in order to train it as a classifier. I am using QIIME2 version 2019.1 on VirtualBox on a Mac. I clicked the link from the data res… --- ## [Qiime2 2018.4 and 2018.11 greengene](https://forum.qiime2.org/t/qiime2-2018-4-and-2018-11-greengene/7250)
**Author:** [@Clara](https://forum.qiime2.org/u/Clara)\ **Replies:** 3\ **Last updated:** [December 4, 2018, 2:27pm UTC](https://forum.qiime2.org/t/qiime2-2018-4-and-2018-11-greengene/7250 "2018-12-04T14:27:02Z")
Hi there, I have a question here, previously when I analysed my sequencing data, in the step where I generated my otu table, I used greengene in the version 2018.4. However, when I re-run my qiime2, the same step has be… --- ## [Finding the right greengenes files for training a classifier](https://forum.qiime2.org/t/finding-the-right-greengenes-files-for-training-a-classifier/5224)
**Author:** [@elaheahmadi](https://forum.qiime2.org/u/elaheahmadi)\ **Replies:** 1\ **Last updated:** [July 24, 2018, 7:44pm UTC](https://forum.qiime2.org/t/finding-the-right-greengenes-files-for-training-a-classifier/5224 "2018-07-24T19:44:23Z")
Dear Mehrbod thank you for guide me I already read overview tutorial but With carelessness and I understand now. I have another question. I do Taxonomic analysis exactly matching with moving pictures tutorial but I use … --- ## [Greengenes Tree Download With Branch Lengths](https://forum.qiime2.org/t/greengenes-tree-download-with-branch-lengths/3329)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 4\ **Last updated:** [March 7, 2018, 6:44am UTC](https://forum.qiime2.org/t/greengenes-tree-download-with-branch-lengths/3329 "2018-03-07T06:44:46Z")
How can I get the 97% GG tree that has branch lengths? Also is there a version I can download that is already a qza file? Thanks! --- ## [I want to change my OTU id into gg\_13\_8 OTU ID](https://forum.qiime2.org/t/i-want-to-change-my-otu-id-into-gg-13-8-otu-id/3175)
**Author:** [@sumujin1](https://forum.qiime2.org/u/sumujin1)\ **Replies:** 1\ **Last updated:** [February 23, 2018, 5:59pm UTC](https://forum.qiime2.org/t/i-want-to-change-my-otu-id-into-gg-13-8-otu-id/3175 "2018-02-23T17:59:30Z")
I got my feature-table using qiime2 with gg\_13\_8 database.In the feature-table the line of OTU id is like ff722dd07d0c077843dbfd89d3793bae,but in the gg\_13\_8 database the line of OTU ID is like 187144.What can i do to ch… --- ## [Loading Greengenes tree in iTOL](https://forum.qiime2.org/t/loading-greengenes-tree-in-itol/2319)
**Author:** [@Richard\_Rodrigues](https://forum.qiime2.org/u/Richard_Rodrigues)\ **Replies:** 10\ **Last updated:** [February 13, 2018, 9:48pm UTC](https://forum.qiime2.org/t/loading-greengenes-tree-in-itol/2319 "2018-02-13T21:48:30Z")
Hi, Did anyone figure out the solution for this? Basically, 97\_otus tree can be visualized in ITOL, but it seems the internal ids and annotation already in the tree are not being recognized by ITOL. Adding an external a… --- ## [How to map SILVA and GG 13\_8 ids to NCBI or IMG ids?](https://forum.qiime2.org/t/how-to-map-silva-and-gg-13-8-ids-to-ncbi-or-img-ids/2809)
**Author:** [@ecolog](https://forum.qiime2.org/u/ecolog)\ **Replies:** 4\ **Last updated:** [February 5, 2018, 4:42pm UTC](https://forum.qiime2.org/t/how-to-map-silva-and-gg-13-8-ids-to-ncbi-or-img-ids/2809 "2018-02-05T16:42:59Z")
If I have a SILVA latest release (132?) or GG 13\_8 taxonomy Ids how can I get the corresponding match to NCBI or IMG databases? I don't want to rely only in the taxonomy per se. I found a GG 13\_5 file "gg\_13\_5\_accession… --- ## [Combine different reference sequences databases](https://forum.qiime2.org/t/combine-different-reference-sequences-databases/2853)
**Author:** [@jacorvar](https://forum.qiime2.org/u/jacorvar)\ **Replies:** 1\ **Last updated:** [February 3, 2018, 2:53pm UTC](https://forum.qiime2.org/t/combine-different-reference-sequences-databases/2853 "2018-02-03T14:53:07Z")
Hi I'm a newbie with QIIME2 and would like to analyse the diversity of a microbiome. In my particular case, I am not only interested in bacteria, but also in fungii and other microorganisms. For this reason, I merged the… --- ## [Feature-classifier error during training](https://forum.qiime2.org/t/feature-classifier-error-during-training/2653)
**Author:** [@leahtee](https://forum.qiime2.org/u/leahtee)\ **Replies:** 8\ **Last updated:** [January 21, 2018, 11:05pm UTC](https://forum.qiime2.org/t/feature-classifier-error-during-training/2653 "2018-01-21T23:05:19Z")
Hey all, I'm currently using the "Moving Pictures" tutorial to help me analyze my own data, and have gotten to the stage where I try to train my feature classifier on the 341F/805R primers for my current data set. qiim… --- ## [SILVA vs Greengenes](https://forum.qiime2.org/t/silva-vs-greengenes/2404)
**Author:** [@hongweiyin](https://forum.qiime2.org/u/hongweiyin)\ **Replies:** 1\ **Last updated:** [January 3, 2018, 4:28pm UTC](https://forum.qiime2.org/t/silva-vs-greengenes/2404 "2018-01-03T16:28:38Z")
Hi @thermokarst Thank you for your advices. i have done it as your advices,and it work well .i have some questions about you classifier,why did you use the silva database since the greegene database have not updated fiv… --- ## [What is the difference between Greengenes and SILVA?](https://forum.qiime2.org/t/what-is-the-difference-between-greengenes-and-silva/1560)
**Author:** [@Aqleem12](https://forum.qiime2.org/u/Aqleem12)\ **Replies:** 4\ **Last updated:** [October 27, 2017, 8:34am UTC](https://forum.qiime2.org/t/what-is-the-difference-between-greengenes-and-silva/1560 "2017-10-27T08:34:37Z")
Dear Sir, Thank you for your support. It took me to 12 hours to set my classifier(Greengenes99%OTS) the recent one. I used the commands that you have sent to me. Every thing is fine now. Finally I got ref.seqs.qza file.… --- ## [Classifier Training Questions](https://forum.qiime2.org/t/classifier-training-questions/1162)
**Author:** [@hongwei2017](https://forum.qiime2.org/u/hongwei2017)\ **Replies:** 2\ **Last updated:** [September 7, 2017, 3:39am UTC](https://forum.qiime2.org/t/classifier-training-questions/1162 "2017-09-07T03:39:39Z")
Hi @thermokarst Can I ask one question about training my classifier? I've downloaded references from the resource page for greengene. There are different folders inside the unzip folder: (1) otus (2) rep\_set (3) rep\_s… --- ## [Training new feature classifier](https://forum.qiime2.org/t/training-new-feature-classifier/1047)
**Author:** [@Bing](https://forum.qiime2.org/u/Bing)\ **Replies:** 4\ **Last updated:** [August 23, 2017, 5:34pm UTC](https://forum.qiime2.org/t/training-new-feature-classifier/1047 "2017-08-23T17:34:28Z")
We are training feature classifiers for the 16S V3-V4 regions. I noticed the Greengenes database (85\_OTU.fasta) listed in the tutorial is from 2013, right? Is there a more updated database available for the training of f… [Next page](https://forum.qiime2.org/tag/greengenes/59.md?match_all_tags=true&page=1&tags%5B%5D=greengenes)