# \#bracken **URL:** https://help.galaxyproject.org/tag/bracken/600.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Adding nt\_core db to Bracken and related workflow tools](https://help.galaxyproject.org/t/adding-nt-core-db-to-bracken-and-related-workflow-tools/14533)
**Author:** [@Laura\_Peirson](https://help.galaxyproject.org/u/Laura_Peirson)\ **Replies:** 8\ **Last updated:** [June 17, 2026, 9:24pm UTC](https://help.galaxyproject.org/t/adding-nt-core-db-to-bracken-and-related-workflow-tools/14533 "2026-06-17T21:24:38Z")
Hello, I have used Kraken2 with the nt\_core database to classify bacteria as well as the metazoa I need. I want to use Bracken. However, the nt\_core database is not an option. I selected the PlusPF (Version 2024-01-12, … --- ## [Eukaryote taxonomic classification reference database options](https://help.galaxyproject.org/t/eukaryote-taxonomic-classification-reference-database-options/14162)
**Author:** [@Laura\_Peirson](https://help.galaxyproject.org/u/Laura_Peirson)\ **Replies:** 13\ **Last updated:** [February 19, 2025, 6:59pm UTC](https://help.galaxyproject.org/t/eukaryote-taxonomic-classification-reference-database-options/14162 "2025-02-19T18:59:06Z")
I have Illumina NextSeq 2000 shallow shotgun metagenomic sequences (from fecal samples) that have been quality filtered and trimmed. I need to classify carnivore prey (metazoa), gastrointestinal parasites, bacteria, plan… --- ## [Kraken2 and Bracken databases update](https://help.galaxyproject.org/t/kraken2-and-bracken-databases-update/14738)
**Author:** [@Carlos-Santos](https://help.galaxyproject.org/u/Carlos-Santos)\ **Replies:** 3\ **Last updated:** [February 19, 2025, 6:58pm UTC](https://help.galaxyproject.org/t/kraken2-and-bracken-databases-update/14738 "2025-02-19T18:58:24Z")
Hi, everyone, I hope you’re doing well! Could you kindly update the databases, especially PlusPFP, when you have a chance? I would really appreciate it. Thank you so much! --- ## [Bracken database missed](https://help.galaxyproject.org/t/bracken-database-missed/14789)
**Author:** [@Carlos-Santos](https://help.galaxyproject.org/u/Carlos-Santos)\ **Replies:** 1\ **Last updated:** [February 19, 2025, 6:55pm UTC](https://help.galaxyproject.org/t/bracken-database-missed/14789 "2025-02-19T18:55:51Z")
Please, I need some help. When I looked for a Kraken2-compatible database for Bracken, I couldn’t find one. By the way, the database is: “Prebuilt Refseq indexes: core\_nt (Very large collection, inclusive of GenBank, … --- ## [Tools registered with testtoolshed.g2.bx.psu.edu cannot be installed](https://help.galaxyproject.org/t/tools-registered-with-testtoolshed-g2-bx-psu-edu-cannot-be-installed/12971)
**Author:** [@youyuh48](https://help.galaxyproject.org/u/youyuh48)\ **Replies:** 5\ **Last updated:** [July 19, 2024, 8:36pm UTC](https://help.galaxyproject.org/t/tools-registered-with-testtoolshed-g2-bx-psu-edu-cannot-be-installed/12971 "2024-07-19T20:36:22Z")
Hi, all I can’t install the tools registered on testtoolshed.g2.bx.psu.edu. When I go to https://testtoolshed.g2.bx.psu.edu/ site in my web browser and click on the Contents button I get an error message “Mercurial rep… --- ## [Bracken reference databases update request in order to cover options provided by Kraken2](https://help.galaxyproject.org/t/bracken-reference-databases-update-request-in-order-to-cover-options-provided-by-kraken2/12974)
**Author:** [@Yordan\_Hodzhev](https://help.galaxyproject.org/u/Yordan_Hodzhev)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 4:02pm UTC](https://help.galaxyproject.org/t/bracken-reference-databases-update-request-in-order-to-cover-options-provided-by-kraken2/12974 "2024-07-17T16:02:47Z")
Dear Admins, Could you please update the list of Kmer distribution reference databases for Bracken tool as it is currently in Kraken2 (Galaxy Version 2.1.3+galaxy1): Thus, users can recalculate in Bracken all kinds o… --- ## [Bracken troubleshooting](https://help.galaxyproject.org/t/bracken-troubleshooting/11688)
**Author:** [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Replies:** 6\ **Last updated:** [February 23, 2024, 9:54pm UTC](https://help.galaxyproject.org/t/bracken-troubleshooting/11688 "2024-02-23T21:54:07Z")
Hi everyone, i asked about Bracken not working a few months ago. Apparently it was fixed but i am still getting an error. Here is what my data looks like. What am I doing wrong? I have the Kraken data which is what i nee… --- ## [Bracken database error](https://help.galaxyproject.org/t/bracken-database-error/11218)
**Author:** [@Carlos-Santos](https://help.galaxyproject.org/u/Carlos-Santos)\ **Replies:** 5\ **Last updated:** [December 1, 2023, 12:10pm UTC](https://help.galaxyproject.org/t/bracken-database-error/11218 "2023-12-01T12:10:29Z")
Hi, guys! I have using Kraken2 and Bracken to taxonomic classification of a WGS study. In the Kraken2, I\`ve used the Prebuilt Refseq indexes: PlusPF (Standard plus protozoa and fungi) (Version: 2022-06-07 - Downloaded: … --- ## [Help using braken- Not working](https://help.galaxyproject.org/t/help-using-braken-not-working/11250)
**Author:** [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Replies:** 1\ **Last updated:** [November 30, 2023, 6:53pm UTC](https://help.galaxyproject.org/t/help-using-braken-not-working/11250 "2023-11-30T18:53:34Z")
Hi everyone , I have proccessed nanopore reads and classified taxonamy using Kraken2. Next I would like to use Bracken. Which of the two outputs should I be using? I have tried both but have instantly had an error and I …