# Exporting OTU/ASV and Taxonomy tables (BIOM / CSV) for MicrobiomeAnalyst from Nanopore 16S GTN Tutorial **URL:** \ **Category:** usegalaxy.org support\ **Tags:** gtn-tutorial, kraken2, kraken\_biom, kraken\ **Created:** [August 10, 2026, 2:57am UTC](https://help.galaxyproject.org/t/exporting-otu-asv-and-taxonomy-tables-biom-csv-for-microbiomeanalyst-from-nanopore-16s-gtn-tutorial/18262 "2026-08-10T02:57:50Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![zahir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/zahir/32/6351_2.png) [@zahir](https://help.galaxyproject.org/u/zahir)\ **Post date:** [August 10, 2026, 2:57am UTC](https://help.galaxyproject.org/t/exporting-otu-asv-and-taxonomy-tables-biom-csv-for-microbiomeanalyst-from-nanopore-16s-gtn-tutorial/18262/1 "2026-08-10T02:57:50Z")
Hello Galaxy Community, I am conducting bacterial diversity analysis on sediment samples using the Oxford Nanopore MinION platform for 16S sequencing. Basecalling and demultiplexing were performed using MinKNOW. After uploading the FASTQ files to [usegalaxy.org](http://usegalaxy.org), I am following the “16S Microbial analysis with Nanopore data” GTN tutorial: > **[Microbiome / 16S Microbial analysis with Nanopore data / Hands-on: 16S...](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html#16s-microbial-analysis-with-nanopore-data)** > > A microbiome is the community of microorganisms that can usually be found living together in any given habitat. Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume... Is there a recommended protocol within Galaxy to generate OTU/ASV and taxonomy tables in BIOM, mothur, .txt, or .csv formats? I need these files to import into the MicrobiomeAnalyst Marker Data Profiling module ( [MicrobiomeAnalyst](https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/upload/OtuUploadView.xhtml) ) to conduct downstream diversity analyses, including taxonomic abundance profiling, alpha and beta diversity, and LEfSe analysis. Attached is the example of the OTU table and taxonomy table that I wish I can get Any guidance or assistance on resolving this issue would be greatly appreciated. Thank you! ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/ef334f873a7b38ffd3b700d10faa1cbd5cda792a.png) ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/3817e50c1985f4b422e620c80a757866ca8057d3.png) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [August 10, 2026, 6:44pm UTC](https://help.galaxyproject.org/t/exporting-otu-asv-and-taxonomy-tables-biom-csv-for-microbiomeanalyst-from-nanopore-16s-gtn-tutorial/18262/2 "2026-08-10T18:44:25Z")
> [@zahir](#): > > Is there a recommended protocol within Galaxy to generate OTU/ASV and taxonomy tables in BIOM, mothur, .txt, or .csv formats? Hi @zahir The GTN has examples here: - **Dada2** → [GTN Materials Search](https://galaxyproject.github.io/training-material/search2?query=dada2) (query=dada2) - **Mothur** → [GTN Materials Search](https://galaxyproject.github.io/training-material/search2?query=mothur) (query=mothur) From there, each of those has a workflow template you could adjust to suit exactly what you want to do. You can also search under **Workflows → Public workflows** at any UseGalaxy server to find these same workflows (but without the large context). The IWC is building out the HTP versions still, and contributions would be welcome from community scientists! - [https://iwc.galaxyproject.org/](https://iwc.galaxyproject.org/) I hope this helps to get you oriented and follow up questions are welcome! 🙂 ---
**Author:** ![zahir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/zahir/32/6351_2.png) [@zahir](https://help.galaxyproject.org/u/zahir)\ **Post date:** [August 11, 2026, 5:00am UTC](https://help.galaxyproject.org/t/exporting-otu-asv-and-taxonomy-tables-biom-csv-for-microbiomeanalyst-from-nanopore-16s-gtn-tutorial/18262/3 "2026-08-11T05:00:36Z")
thanks a lot for your suggestions much appreciated it Actually I am still confuse on how can I convert my Kraken2 outputs (Report and Classification) into BIOM file ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [August 11, 2026, 6:23pm UTC](https://help.galaxyproject.org/t/exporting-otu-asv-and-taxonomy-tables-biom-csv-for-microbiomeanalyst-from-nanopore-16s-gtn-tutorial/18262/4 "2026-08-11T18:23:08Z")
Hi @zahir Does this seem like the right tool? - **Kraken-biom** Create BIOM-format tables from kraken output Try a search in the tool panel with “biom” for more examples (from Mothur) or to convert between formats starting from a `tsv` dataset. A search with “kraken” will bring up most for Kraken/Kraken2. If you need to do intermediate manipulations, perhaps for the review steps, we have cheat sheets for Text Manipulations or you can also enter a notebook environment like Jupyter. You should be able to generate [everything you need for the other website](https://www.microbiomeanalyst.ca/docs/DataFormat.xhtml). The workflow would be something like: **Galaxy** 1. → **Porechop** Input: MinKNOW demultiplexed FASTQ 2. → **fastp** Input: trimmed FASTQ 3. → **Kraken2** Input: filtered FASTQ Output: **Kraken2 Report** 4. → **Kraken-biom** Input: Kraken2 Report(s) Output: **BIOM** 5. → **Confirm formats/counts** - [https://www.microbiomeanalyst.ca/docs/DataFormat.xhtml](https://www.microbiomeanalyst.ca/docs/DataFormat.xhtml) - Text Manipulations→ [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=olympics) (query=olympics) - Notebooks → [GTN Materials Search](https://galaxyproject.github.io/training-material/search2?query=jupyter) (query=jupyter) 6. → **Download** data **MicrobiomeAnalyst** 1. **Upload** data (URLs are not supported) * * * Let us know your thoughts and how this works out! Once you know your parameters, you could edit to add in the extra tools to the end of the tutorial’s base workflow. 👨‍🔬