split FASTQ files based on Illumina indexes in the ID

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

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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Hi @agata_s,
currently, there’s not a tool able to perform such operation; I started working on demuxbyname (more information here), since I will provide that functionality. I will try to make it available from the next week.


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