# NanoFilt Tool - Galaxy

**URL:** <https://help.galaxyproject.org/t/nanofilt-tool-galaxy/15946>\
**Category:** usegalaxy.eu support\
**Tags:** single-cell, quality-control, nanoplot\
**Created:** [July 10, 2025, 9:49am UTC](https://help.galaxyproject.org/t/nanofilt-tool-galaxy/15946 "2025-07-10T09:49:33Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![alica\_brodova](https://avatars.discourse-cdn.com/v4/letter/a/8797f3/32.png) [@alica\_brodova](https://help.galaxyproject.org/u/alica_brodova)\
**Post date:** [July 10, 2025, 9:49am UTC](https://help.galaxyproject.org/t/nanofilt-tool-galaxy/15946/1 "2025-07-10T09:49:33Z")

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Hi.

Before two weeks I was at ECDC training. We use NanoFilt tool through Galaxy. Now I can not find it in list of tools. Does it exist here?

Thank you

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**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:** [July 10, 2025, 8:00pm UTC](https://help.galaxyproject.org/t/nanofilt-tool-galaxy/15946/2 "2025-07-10T20:00:37Z")

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Welcome @alica_brodova

These are the two tools I can think of that might be what you are looking for:

- **filtlong** Filtering long reads by quality link at UseGalaxy.eu
- **NanoPlot** Plotting suite for Oxford Nanopore sequencing data and alignments link at UseGalaxy.eu

Are one of these what you are looking for? Were you working at this server during the training? Do the training materials or your account creation emails list a specific server (these should)?

Please let us know if you need more help! 🙂

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**Author:** ![alica\_brodova](https://avatars.discourse-cdn.com/v4/letter/a/8797f3/32.png) [@alica\_brodova](https://help.galaxyproject.org/u/alica_brodova)\
**Post date:** [July 11, 2025, 7:17am UTC](https://help.galaxyproject.org/t/nanofilt-tool-galaxy/15946/3 "2025-07-11T07:17:13Z")

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Thank you for answer.

These tools can not trimm samples based on GC content. Is here any tool which can do it?  
We were working at university server. I think it is reason why I can not find it here.

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**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:** [July 11, 2025, 9:03pm UTC](https://help.galaxyproject.org/t/nanofilt-tool-galaxy/15946/4 "2025-07-11T21:03:40Z")

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Ok, thanks for explaining @alica_brodova

Yes, different tools might be available at different Galaxy servers.

After looking closer: it seems like [NanoFilt was deprecated](https://github.com/wdecoster/nanofilt) – and I found an [older version of a tool wrapper in the ToolShed](https://toolshed.g2.bx.psu.edu/view/leomrtns/nanofilt/a2c318b04f49) based on that. This is not hosted at the public servers (for what are probably technical reasons) and my guess is either ECDC is running a legacy version of Galaxy or has done something else custom to host it.

For now, the current available tool I can think of for _trimming_ Nanopore reads at the public servers is:

- **Porechop** adapter trimmer for Oxford Nanopore reads

For guides about how this works in combination with other tools, we have a very good set of tutorials here. You can also review the Help section on tool forms (scroll down) for short guides, links to external manuals, and direct links to the GTN tutorials that happen to include them.

- Topic category → [Single Cell / Tutorial List](https://training.galaxyproject.org/training-material/topics/single-cell/)
- Search → [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=nanopore) (query=nanopore)

I hope I am actually helping this time, but let me know and please ask if you need more help! 🙂