# split FASTQ files based on Illumina indexes in the ID

**URL:** <https://help.galaxyproject.org/t/split-fastq-files-based-on-illumina-indexes-in-the-id/8190>\
**Category:** usegalaxy.org support\
**Tags:** quality-control\
**Created:** [June 13, 2022, 12:30pm UTC](https://help.galaxyproject.org/t/split-fastq-files-based-on-illumina-indexes-in-the-id/8190 "2022-06-13T12:30:13Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![agata\_s](https://avatars.discourse-cdn.com/v4/letter/a/b9e5f3/32.png) [@agata\_s](https://help.galaxyproject.org/u/agata_s)\
**Post date:** [June 13, 2022, 12:30pm UTC](https://help.galaxyproject.org/t/split-fastq-files-based-on-illumina-indexes-in-the-id/8190/1 "2022-06-13T12:30:13Z")

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Hi,  
I’m looking for a tool/way to extract the barcode from fastq file and to split fastq file into separate fastq files based on the indices. The indices are placed in the sequence ID. Here is the example:

@NB552014:62:HGCLWBGXJ:1:11101:8614:1055 1:N:0:ACTATAAC+TAAGATTA  
GATCGNAAGAGCACACGTCTGAACTCCAGTCACACTA  
+  
AAAAA#EEEAEEEEEEAEE/AEEEEEAE//EE\</A//

Incorrect index sequences were entered in the sample sheet and Illumina demultiplexing filed. I have the fastq files and try to demultiplex on my own…any suggestions, please?

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [June 21, 2022, 12:00pm UTC](https://help.galaxyproject.org/t/split-fastq-files-based-on-illumina-indexes-in-the-id/8190/2 "2022-06-21T12:00:58Z")

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Hi @agata_s,  
currently, there’s not a tool able to perform such operation; I started working on **demuxbyname** (more information [here](https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/46256-efficient-way-to-split-fastq-files-based-on-illumina-indexes-in-the-id?t=56429)), since I will provide that functionality. I will try to make it available from the next week.

Regards

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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:** [September 21, 2022, 9:50pm UTC](https://help.galaxyproject.org/t/split-fastq-files-based-on-illumina-indexes-in-the-id/8190/3 "2022-09-21T21:50:33Z")

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