# How to merge multiple fastq files into one? How do trim low-quality sequences based on Qscore of Nanopore data?

**URL:** <https://help.galaxyproject.org/t/how-to-merge-multiple-fastq-files-into-one-how-do-trim-low-quality-sequences-based-on-qscore-of-nanopore-data/10234>\
**Category:** Uncategorized\
**Tags:** quality-control\
**Created:** [June 13, 2023, 12:37am UTC](https://help.galaxyproject.org/t/how-to-merge-multiple-fastq-files-into-one-how-do-trim-low-quality-sequences-based-on-qscore-of-nanopore-data/10234 "2023-06-13T00:37:44Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Thuy\_Nguyen](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/thuy_nguyen/32/4403_2.png) [@Thuy\_Nguyen](https://help.galaxyproject.org/u/Thuy_Nguyen)\
**Post date:** [June 13, 2023, 12:37am UTC](https://help.galaxyproject.org/t/how-to-merge-multiple-fastq-files-into-one-how-do-trim-low-quality-sequences-based-on-qscore-of-nanopore-data/10234/1 "2023-06-13T00:37:44Z")

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Dear all,

I am a new user who is working on Nanopore data. I have many fastq files for each individual sample, but I do not know how to merge these files. In addition, I am also looking for a tool for trimming low-quality sequences based on Qscore before mapping. Is there any tool compatible with Nanapore for this work?

I really appreciate any help you can provide.

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**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [June 13, 2023, 3:35am UTC](https://help.galaxyproject.org/t/how-to-merge-multiple-fastq-files-into-one-how-do-trim-low-quality-sequences-based-on-qscore-of-nanopore-data/10234/2 "2023-06-13T03:35:04Z")

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Hi @Thuy_Nguyen  
check GTN tutorials:

> **[Galaxy Training: Genome Assembly of MRSA using Oxford Nanopore MinION Data](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/tutorial.html#quality-control)**
>
> DNA sequence data has become an indispensable tool for Mo...

> **[Galaxy Training: Quality Control](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html#assess-quality-with-nanoplot---long-reads-only)**
>
> Analyses of sequences

For merging try Concatenate.

Hope that helps.

Igor

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**Author:** ![Thuy\_Nguyen](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/thuy_nguyen/32/4403_2.png) [@Thuy\_Nguyen](https://help.galaxyproject.org/u/Thuy_Nguyen)\
**Post date:** [June 13, 2023, 11:22am UTC](https://help.galaxyproject.org/t/how-to-merge-multiple-fastq-files-into-one-how-do-trim-low-quality-sequences-based-on-qscore-of-nanopore-data/10234/3 "2023-06-13T11:22:04Z")

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Hi @igor  
Thank you for your prompt sharing. It is so helpful.

Thuy