# Illumina fastq (pair-end) file conversion to fasta file

**URL:** <https://help.galaxyproject.org/t/illumina-fastq-pair-end-file-conversion-to-fasta-file/14934>\
**Category:** usegalaxy.be support\
**Tags:** troubleshooting\
**Created:** [March 6, 2025, 4:10pm UTC](https://help.galaxyproject.org/t/illumina-fastq-pair-end-file-conversion-to-fasta-file/14934 "2025-03-06T16:10:44Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![clahey](https://avatars.discourse-cdn.com/v4/letter/c/6de8d8/32.png) [@clahey](https://help.galaxyproject.org/u/clahey)\
**Post date:** [March 6, 2025, 4:10pm UTC](https://help.galaxyproject.org/t/illumina-fastq-pair-end-file-conversion-to-fasta-file/14934/1 "2025-03-06T16:10:44Z")

</div>

Hello,  
I want to combine pair-end illumina fastq file and convert them into a single fasta file.

---

<div class="post-metadata">

**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:** [March 7, 2025, 6:50pm UTC](https://help.galaxyproject.org/t/illumina-fastq-pair-end-file-conversion-to-fasta-file/14934/2 "2025-03-07T18:50:19Z")

</div>

Welcome @clahey

You can use tools to concatenate sequences together and then convert the format but I’m wondering what your larger goal is. Are you concerned about redundancy? Do you want to assemble the reads? Do the reads represent RNA or DNA? Are these short reads?

We have tutorials here that may help you to get oriented.

> **[Galaxy Training!](https://training.galaxyproject.org/training-material/)**
>
> Collection of tutorials developed and maintained by the worldwide Galaxy community

Maybe try a search with keywords, or navigate by the different analysis domains?

This is one example where the initial fastq reads were assembled into in a consensus fasta format.

> **[Assembly / Chloroplast genome assembly / Hands-on: Chloroplast genome assembly](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/tutorial.html)**
>
> DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species....

Hope this helps and you can ask follow up questions! 🙂

---

<div class="post-metadata">

**Author:** ![clahey](https://avatars.discourse-cdn.com/v4/letter/c/6de8d8/32.png) [@clahey](https://help.galaxyproject.org/u/clahey)\
**Post date:** [March 7, 2025, 7:07pm UTC](https://help.galaxyproject.org/t/illumina-fastq-pair-end-file-conversion-to-fasta-file/14934/3 "2025-03-07T19:07:07Z")

</div>

These links/tutorials are very helpful. Thank you Jennifer