# \#metagenomics **URL:** https://help.galaxyproject.org/tag/metagenomics/98.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Pre.cluster (mothur) empty outputs: consider using groups! Please see tutorial example](https://help.galaxyproject.org/t/pre-cluster-mothur-empty-outputs-consider-using-groups-please-see-tutorial-example/18347)
**Author:** [@Heba\_Hathout](https://help.galaxyproject.org/u/Heba_Hathout)\ **Replies:** 1\ **Last updated:** [August 27, 2026, 4:27pm UTC](https://help.galaxyproject.org/t/pre-cluster-mothur-empty-outputs-consider-using-groups-please-see-tutorial-example/18347 "2026-08-27T16:27:53Z")
Server URL: usegalaxy dot org I’m running the Pre.cluster tool (mothur, Galaxy Version 1.39.5.0) on a 16S mothur pipeline (23 samples, RedSeaSeawater\_16S\_Mothur pipeline history). The job has been stuck in “running” s… --- ## [Ribosomal Database Project and Greengenes Database for Metagenomic Analysis](https://help.galaxyproject.org/t/ribosomal-database-project-and-greengenes-database-for-metagenomic-analysis/18212)
**Author:** [@Vyenge\_Erre\_Gayosa](https://help.galaxyproject.org/u/Vyenge_Erre_Gayosa)\ **Replies:** 2\ **Last updated:** [July 28, 2026, 6:18pm UTC](https://help.galaxyproject.org/t/ribosomal-database-project-and-greengenes-database-for-metagenomic-analysis/18212 "2026-07-28T18:18:25Z")
Hello everyone, I am new to metagenomic analysis using Galaxy and would like to ask about reference databases for taxonomic classification. Is it possible to upload and use custom reference databases, such as the Ribos… --- ## [How to use MEGAHIT](https://help.galaxyproject.org/t/how-to-use-megahit/12155)
**Author:** [@MarwahSabo](https://help.galaxyproject.org/u/MarwahSabo)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 1:59am UTC](https://help.galaxyproject.org/t/how-to-use-megahit/12155 "2026-04-18T01:59:25Z")
hallow I’m trying to assembly my data by megahit. it cannot run don’t know why anyone can helps. --- ## [Taxonomy workflows: reads to taxa](https://help.galaxyproject.org/t/taxonomy-workflows-reads-to-taxa/16541)
**Author:** [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\ **Replies:** 8\ **Last updated:** [December 31, 2025, 5:45pm UTC](https://help.galaxyproject.org/t/taxonomy-workflows-reads-to-taxa/16541 "2025-12-31T17:45:14Z")
Hi Jemma, I have some samples being sequenced. These are for soil fungi eDNA metarcoding. On NCBI I have found and downloaded a FASTQ file (2MB) of the type I will be using. Sequences will be about 300bp long. I woul… --- ## [Basic eDNA worklow](https://help.galaxyproject.org/t/basic-edna-worklow/14340)
**Author:** [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\ **Replies:** 4\ **Last updated:** [January 8, 2025, 11:36am UTC](https://help.galaxyproject.org/t/basic-edna-worklow/14340 "2025-01-08T11:36:31Z")
Hi, would like to use Galaxy to build an eDNA workflow pipeline to process Metabarcoding data from Illumina. Is this possible or are there other open source tools available to do this ? Basic steps needed : Read demult… --- ## [DRAM distill: Error while running](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665)
**Author:** [@Mohanchaitanya](https://help.galaxyproject.org/u/Mohanchaitanya)\ **Replies:** 5\ **Last updated:** [September 22, 2025, 8:50pm UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665 "2025-09-22T20:50:40Z")
DRAM annotate ran successfully, but the output only includes only positional data (start/end coordinates, etc.), gene position, rRNAs, and tRNAs. It does NOT contain functional annotation columns like kegg\_id, uniref\_id,… --- ## [Visualize with Krona error? Use Krona Pie Chart instead!](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111)
**Author:** [@Barry](https://help.galaxyproject.org/u/Barry)\ **Replies:** 12\ **Last updated:** [August 6, 2025, 10:52pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111 "2025-08-06T22:52:42Z")
I am trying to plot a Krona chart from a Kraken2 report, but I keep getting the following error: /cvmfs/main.galaxyproject.org/shed\_tools/toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona\_text/b14f1444e464/krona\_text/… --- ## [Pcoa. phylip-formatted distance matrix](https://help.galaxyproject.org/t/pcoa-phylip-formatted-distance-matrix/15717)
**Author:** [@Tahmine\_Aldaghi](https://help.galaxyproject.org/u/Tahmine_Aldaghi)\ **Replies:** 3\ **Last updated:** [July 23, 2025, 6:58pm UTC](https://help.galaxyproject.org/t/pcoa-phylip-formatted-distance-matrix/15717 "2025-07-23T18:58:13Z")
How can I make a phylip-formatted distance matrix? I need it for beta diversity analysis --- ## [MOTHUR filter.seqs help](https://help.galaxyproject.org/t/mothur-filter-seqs-help/15395)
**Author:** [@ameliak](https://help.galaxyproject.org/u/ameliak)\ **Replies:** 3\ **Last updated:** [July 23, 2025, 6:49pm UTC](https://help.galaxyproject.org/t/mothur-filter-seqs-help/15395 "2025-07-23T18:49:12Z")
Hi everyone, I’ve been following the mothur tutorial to perform my metagenomics analysis, and having trouble with the filter.seqs step in the data cleaning after sequence allignment. When I use the settings as in the t… --- ## [Mobile Genetic Elements](https://help.galaxyproject.org/t/mobile-genetic-elements/15340)
**Author:** [@sm9412](https://help.galaxyproject.org/u/sm9412)\ **Replies:** 2\ **Last updated:** [May 2, 2025, 10:41am UTC](https://help.galaxyproject.org/t/mobile-genetic-elements/15340 "2025-05-02T10:41:39Z")
Hi, I am doing metagenomics analysis for a set of samples. I want to look for mobile genetic elements (Integrons, transposons) in the reads, but am unable to find any tool for the same in Galaxy. Can someone help me wit… --- ## [Troubleshooting: Krona Pie chart display](https://help.galaxyproject.org/t/troubleshooting-krona-pie-chart-display/14519)
**Author:** [@vaandio](https://help.galaxyproject.org/u/vaandio)\ **Replies:** 6\ **Last updated:** [March 17, 2025, 4:57pm UTC](https://help.galaxyproject.org/t/troubleshooting-krona-pie-chart-display/14519 "2025-03-17T16:57:56Z")
Hi. I am using galaxy at https://usegalaxy.org/ I have a similar problem that was discussed above. I am working on a metagenomics project and trying to use Krona pie chart tool to visualize my data. In recent runs, it … --- ## [I attempted to run LOTUS2 on the Galaxy server multiple times, but the job failed](https://help.galaxyproject.org/t/i-attempted-to-run-lotus2-on-the-galaxy-server-multiple-times-but-the-job-failed/15034)
**Author:** [@Latif\_khan\_shamozai](https://help.galaxyproject.org/u/Latif_khan_shamozai)\ **Replies:** 1\ **Last updated:** [March 17, 2025, 4:28pm UTC](https://help.galaxyproject.org/t/i-attempted-to-run-lotus2-on-the-galaxy-server-multiple-times-but-the-job-failed/15034 "2025-03-17T16:28:25Z")
I attempted to run LOTUS2 on the Galaxy server multiple times, but the job failed each time with an error. I have carefully followed the required steps, ensuring that: My data is correctly formatted as paired-end ITS … --- ## [GTDB-Tk Classify genomes](https://help.galaxyproject.org/t/gtdb-tk-classify-genomes/12578)
**Author:** [@matamela27](https://help.galaxyproject.org/u/matamela27)\ **Replies:** 2\ **Last updated:** [February 14, 2025, 8:55pm UTC](https://help.galaxyproject.org/t/gtdb-tk-classify-genomes/12578 "2025-02-14T20:55:03Z")
Does GTDB-Tk classify metagenomic contigs? --- ## [Downloading ASV table for microbial community network analysis](https://help.galaxyproject.org/t/downloading-asv-table-for-microbial-community-network-analysis/14371)
**Author:** [@Ranjith\_Kumar](https://help.galaxyproject.org/u/Ranjith_Kumar)\ **Replies:** 14\ **Last updated:** [January 26, 2025, 8:11am UTC](https://help.galaxyproject.org/t/downloading-asv-table-for-microbial-community-network-analysis/14371 "2025-01-26T08:11:31Z")
In the tutorial, building an amplicon sequence variant (ASV) table from 16S data using DADA2, could you please specify the steps for downloading the ASV table (similar to OTU) that will be used for further microbial comm… --- ## [Issue with Krona pie chart tool](https://help.galaxyproject.org/t/issue-with-krona-pie-chart-tool/350)
**Author:** [@Catfishboy2112](https://help.galaxyproject.org/u/Catfishboy2112)\ **Replies:** 10\ **Last updated:** [June 30, 2019, 10:35am UTC](https://help.galaxyproject.org/t/issue-with-krona-pie-chart-tool/350 "2019-06-30T10:35:25Z")
I am working on a metagenomics project and trying to use Krona pie chart tool to visualize my data. In recent runs, it stopped generating the chart. Instead, it began to display hypertext coding for the HTML. Is there… --- ## [Kraken2 Databse for 16s full length metagenomics](https://help.galaxyproject.org/t/kraken2-databse-for-16s-full-length-metagenomics/14241)
**Author:** [@Azmi\_Zaki\_Waliudin\_A](https://help.galaxyproject.org/u/Azmi_Zaki_Waliudin_A)\ **Replies:** 1\ **Last updated:** [January 6, 2025, 10:43pm UTC](https://help.galaxyproject.org/t/kraken2-databse-for-16s-full-length-metagenomics/14241 "2025-01-06T22:43:11Z")
Hi! I have 16s full length metagenome sequences. I would do taxonomic classification using Kraken2. I want to calssify my sequences to species level. But, when I use all database in Kraken2, I only get few species. Do yo… --- ## [16S V3/V4 database needed](https://help.galaxyproject.org/t/16s-v3-v4-database-needed/14230)
**Author:** [@biologisthurkan](https://help.galaxyproject.org/u/biologisthurkan)\ **Replies:** 6\ **Last updated:** [December 28, 2024, 9:17pm UTC](https://help.galaxyproject.org/t/16s-v3-v4-database-needed/14230 "2024-12-28T21:17:43Z")
Hi there, I need reference silva database for V3/V4 region already trimmed. Anyone can help? Thank you. --- ## [Microbiome Global Picture Phinch BIOM1 format](https://help.galaxyproject.org/t/microbiome-global-picture-phinch-biom1-format/14144)
**Author:** [@yogesh\_parmessur](https://help.galaxyproject.org/u/yogesh_parmessur)\ **Replies:** 3\ **Last updated:** [December 16, 2024, 6:45am UTC](https://help.galaxyproject.org/t/microbiome-global-picture-phinch-biom1-format/14144 "2024-12-16T06:45:03Z")
Hi I am into The Global Picture tutorial Hands-on: Analyses of metagenomics data - The global picture / Analyses of metagenomics data - The global picture / Microbiome. The format from the BIOM1 file generated is 0.9.… --- ## [Unclassified, Eukaryote data in Dada2 for ASV.](https://help.galaxyproject.org/t/unclassified-eukaryote-data-in-dada2-for-asv/14054)
**Author:** [@Shweta.203](https://help.galaxyproject.org/u/Shweta.203)\ **Replies:** 2\ **Last updated:** [December 12, 2024, 10:52am UTC](https://help.galaxyproject.org/t/unclassified-eukaryote-data-in-dada2-for-asv/14054 "2024-12-12T10:52:01Z")
Hi Everyone, I have used DADA2 for generating ASV files following tutorial.Hands-on: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 / Building an amplicon sequence variant (ASV) table from 1… --- ## [Kraken2 database](https://help.galaxyproject.org/t/kraken2-database/11734)
**Author:** [@mycojon](https://help.galaxyproject.org/u/mycojon)\ **Replies:** 24\ **Last updated:** [November 26, 2024, 1:12am UTC](https://help.galaxyproject.org/t/kraken2-database/11734 "2024-11-26T01:12:49Z")
Is there any galaxy site that has the kraken2 nt-database 719 GB installed?? I keep running into problems where the databases are missing some of the species in my samples. Also, I see that kraken2 can work similar to … --- ## [Sample number for galaxy mothur](https://help.galaxyproject.org/t/sample-number-for-galaxy-mothur/14053)
**Author:** [@Shweta.203](https://help.galaxyproject.org/u/Shweta.203)\ **Replies:** 1\ **Last updated:** [December 4, 2024, 5:30pm UTC](https://help.galaxyproject.org/t/sample-number-for-galaxy-mothur/14053 "2024-12-04T17:30:15Z")
Hi everyone, I have one query regarding the samples number when using mothur tool. I have used mothur for 16s metagenomics data analysis for 46 samples, 2 samples and 4 samples by following the tutorials. For visualiza… --- ## [Nanopore taxonomy analysis on MetaPhlan](https://help.galaxyproject.org/t/nanopore-taxonomy-analysis-on-metaphlan/14015)
**Author:** [@Lily\_ofthepond](https://help.galaxyproject.org/u/Lily_ofthepond)\ **Replies:** 2\ **Last updated:** [November 28, 2024, 3:17pm UTC](https://help.galaxyproject.org/t/nanopore-taxonomy-analysis-on-metaphlan/14015 "2024-11-28T15:17:36Z")
Hi, I seem to run into issues running MetaPhlan on cleaned (fastp) Nanopore fastq files of metagenomes. I have already tried different MetaPhlan tool versions, lowering the MapQ teshold, different database, different fi… --- ## [Troubleshooting Mothur pipeline: Sub.sample](https://help.galaxyproject.org/t/troubleshooting-mothur-pipeline-sub-sample/13992)
**Author:** [@Farah\_Zahoor\_RAJPUT](https://help.galaxyproject.org/u/Farah_Zahoor_RAJPUT)\ **Replies:** 5\ **Last updated:** [November 28, 2024, 2:07pm UTC](https://help.galaxyproject.org/t/troubleshooting-mothur-pipeline-sub-sample/13992 "2024-11-28T14:07:53Z")
This problem was solved ? I am having the same problem , Please guide me. --- ## [Assistance with resolving Sub.sample tool output error](https://help.galaxyproject.org/t/assistance-with-resolving-sub-sample-tool-output-error/2286)
**Author:** [@Erica\_Dasi](https://help.galaxyproject.org/u/Erica_Dasi)\ **Replies:** 10\ **Last updated:** [October 30, 2019, 10:15am UTC](https://help.galaxyproject.org/t/assistance-with-resolving-sub-sample-tool-output-error/2286 "2019-10-30T10:15:45Z")
Greetings, I am currently using the Galaxy Europe platform to analyze 16S sequencing data, while using the 16S Microbial Analysis tutorial (https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials… --- ## [How to add SILVA\_138.2 latets as a reference to align.seqs tool in GALAXY Server?](https://help.galaxyproject.org/t/how-to-add-silva-138-2-latets-as-a-reference-to-align-seqs-tool-in-galaxy-server/13597)
**Author:** [@Ahmer](https://help.galaxyproject.org/u/Ahmer)\ **Replies:** 3\ **Last updated:** [October 7, 2024, 5:48pm UTC](https://help.galaxyproject.org/t/how-to-add-silva-138-2-latets-as-a-reference-to-align-seqs-tool-in-galaxy-server/13597 "2024-10-07T17:48:56Z")
Hello, I am doing 16s rRNA (V5-V7 region) metagenomics analysis. I downloaded SILVA\_138.2\_SSURef\_NR99\_tax\_silva.fasta.gz from (https://www.arb-silva.de/fileadmin/silva\_databases/release\_138\_2/Exports/SILVA\_138.2\_SSURef\_N… --- ## [comparison between groups](https://help.galaxyproject.org/t/comparison-between-groups/13862)
**Author:** [@yasmeen\_hisham](https://help.galaxyproject.org/u/yasmeen_hisham)\ **Replies:** 1\ **Last updated:** [November 8, 2024, 9:54pm UTC](https://help.galaxyproject.org/t/comparison-between-groups/13862 "2024-11-08T21:54:48Z")
hello , i have used mothur and created Krona pie chart , what i use in galaxy to perform comparison between groups to explain whats going on between the groups and link all figures together whats your advice --- ## [Align.seq Error 153](https://help.galaxyproject.org/t/align-seq-error-153/13690)
**Author:** [@AidanJ](https://help.galaxyproject.org/u/AidanJ)\ **Replies:** 1\ **Last updated:** [October 20, 2024, 12:18am UTC](https://help.galaxyproject.org/t/align-seq-error-153/13690 "2024-10-20T00:18:50Z")
Fairly new to all this DNA analysis (not my background), I’ve gone through the 16S Microbial Analysis with mothur (extended) tutorial and had no issues. I’ve now started work on my own data (analysing 16S RNA region from… --- ## [Error with make.contigs tool in 16s microbial analysis with mothur tuto](https://help.galaxyproject.org/t/error-with-make-contigs-tool-in-16s-microbial-analysis-with-mothur-tuto/13572)
**Author:** [@lore77](https://help.galaxyproject.org/u/lore77)\ **Replies:** 15\ **Last updated:** [October 15, 2024, 7:43am UTC](https://help.galaxyproject.org/t/error-with-make-contigs-tool-in-16s-microbial-analysis-with-mothur-tuto/13572 "2024-10-15T07:43:57Z")
Hello, I am going thrugh this tutorial in the training website and after trying with the dataset from the training (the dada did not upload, I made another post about that) I decided to try with my data, but now I have a… --- ## [Adding SILVA 138 to Mothur](https://help.galaxyproject.org/t/adding-silva-138-to-mothur/4312)
**Author:** [@siuguy](https://help.galaxyproject.org/u/siuguy)\ **Replies:** 3\ **Last updated:** [October 4, 2024, 6:05pm UTC](https://help.galaxyproject.org/t/adding-silva-138-to-mothur/4312 "2024-10-04T18:05:33Z")
Hello, I am new to galaxy, so this question may sound simple… I am following the 16S analysis tutorial (https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html), bu… --- ## [How can i use SILVA\_138.2 latets as a reference to align.seqs tool in GALAXY Server?](https://help.galaxyproject.org/t/how-can-i-use-silva-138-2-latets-as-a-reference-to-align-seqs-tool-in-galaxy-server/13599)
**Author:** [@Ahmer](https://help.galaxyproject.org/u/Ahmer)\ **Replies:** 1\ **Last updated:** [October 4, 2024, 6:03pm UTC](https://help.galaxyproject.org/t/how-can-i-use-silva-138-2-latets-as-a-reference-to-align-seqs-tool-in-galaxy-server/13599 "2024-10-04T18:03:33Z")
Hello, I am doing 16s rRNA (V5-V7 region) metagenomics analysis. I downloaded SILVA\_138.2\_SSURef\_NR99\_tax\_silva.fasta.gz from (https://www.arb-silva.de/fileadmin/silva\_databases/release\_138\_2/Exports/SILVA\_138.2\_SSURef\_N… [Next page](https://help.galaxyproject.org/tag/metagenomics/98.md?match_all_tags=true&page=1&tags%5B%5D=metagenomics)