# Request: Add host-decontamination tool (KneadData) or a comparable tool on Galaxy.eu for human shotgun metagenomics preprocessing **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** workflow, mapping, tool-request, iwc-workflows, humann\ **Created:** [November 5, 2025, 2:53pm UTC](https://help.galaxyproject.org/t/request-add-host-decontamination-tool-kneaddata-or-a-comparable-tool-on-galaxy-eu-for-human-shotgun-metagenomics-preprocessing/16472 "2025-11-05T14:53:51Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![sri\_microbiome](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sri_microbiome/32/6818_2.png) [@sri\_microbiome](https://help.galaxyproject.org/u/sri_microbiome)\ **Post date:** [November 5, 2025, 2:53pm UTC](https://help.galaxyproject.org/t/request-add-host-decontamination-tool-kneaddata-or-a-comparable-tool-on-galaxy-eu-for-human-shotgun-metagenomics-preprocessing/16472/1 "2025-11-05T14:53:51Z")
Hello Support Team, I plan to pre- process human stool shotgun metagenomes on [Galaxy.eu](http://Galaxy.eu) and need a host-decontamination step before MetaPhlAn/HUMAnN. I couldn’t find **KneadData** in the tool panel,so I can’t filter human reads Could you please let me know if it is possible from the admin team to Install **KneadData** or recommend the preferred [Galaxy.eu](http://Galaxy.eu) tool for host read removal on human fecal shotgun metagenomics fastq files ? My intended workflow within [galaxy.eu](http://galaxy.eu) is: Cutadapt → Host decontamination (KneadData or your recommendation ) → MetaPhlAn 3 → HUMAnN 3 Thanks a lot for your help and attention to my tool requests Best regards, Sri ---
**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:** [November 5, 2025, 9:22pm UTC](https://help.galaxyproject.org/t/request-add-host-decontamination-tool-kneaddata-or-a-comparable-tool-on-galaxy-eu-for-human-shotgun-metagenomics-preprocessing/16472/2 "2025-11-05T21:22:54Z")
Hi @sri_microbiome This is the protocol you are following, correct? - [GitHub - biobakery/biobakery\_workflows: bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.](https://github.com/biobakery/biobakery_workflows?tab=readme-ov-file#whole-metagenome-shotgun-wmgx) (#whole-metagenome-shotgun-wmgx) - [KneadData – The Huttenhower Lab](https://huttenhower.sph.harvard.edu/kneaddata/) I don’t think the Biobakery team has wrapped this for Galaxy yet. I don’t see it at their server or in the ToolShed, and I don’t see these workflow in the public Shared Data → Workflows area either. - [http://galaxy.biobakery.org/](http://galaxy.biobakery.org/) - [https://toolshed.g2.bx.psu.edu/](https://toolshed.g2.bx.psu.edu/) Now, from what I understand, this protocol is more of a _workflow_ than a distinct novel tool but I suppose it could be all combined on a Galaxy tool form. I checked the Biobakery forum and didn’t find any questions about this yet, or I missed the discussion. - [Search results for 'kneaddata galaxy' - The bioBakery help forum](https://forum.biobakery.org/search?q=kneaddata%20galaxy) **What to try** 1. **For immediate processing** , Run the Bowtie2 and other mappings directly in your own workflow. All of these tools are available and using a custom genome is possible. You don’t need to index it – Bowtie2 indexes are created at runtime. You only need the fasta in your history. 2. For later use, ask a question at the Biobakery forum about plans for this tool. 3. Big picture: Someone should put the **wmgx** protocol all together into an IWC workflow! [https://iwc.galaxyproject.org/](https://iwc.galaxyproject.org/) I’m just mentioning it in case you or someone else reading is interested. These tools are somewhat new, so maybe Galaxy workflows are already being planned. The Biobakery forum would be the place to ask about this as well. We would be interested in what happens, so if you want to crosslink the topic (add ours to their forum, then post back here with their link) that would be useful! I’m also going to ask at the [IUC matrix chat](https://matrix.to/#/!IiwsCcdJfpxqyHPPre:gitter.im/$-Kx0xoSkFu3ST-XKPwS7t6ntIMltw7kf-zI9wnnxPTw?via=gitter.im&via=matrix.org&via=matrix.midnightmechanism.xyz) to see if anyone knows more but let’s keep this part of the conversation here. Hope this helps! 🙂 ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [November 6, 2025, 7:23am UTC](https://help.galaxyproject.org/t/request-add-host-decontamination-tool-kneaddata-or-a-comparable-tool-on-galaxy-eu-for-human-shotgun-metagenomics-preprocessing/16472/3 "2025-11-06T07:23:38Z")
More discussion has happened in the [microgalaxy matrix chat](https://matrix.to/#/!IgSDomPGpQMyKaYClI:gitter.im/$Fi7wccbiSK6eZfRWV83B7adykcEw00AVIXtdRE9pdOs). Still a good idea to leave this thread here open.