dmeultiplexing fastq files that contain multiple samples


I hope someone can point me to the right bioinformatics tool to solve the following:

I have fastq files (12 foward (e.g. xxxx_2_1.fastq) and 12 backward (e.g. xxxx_2_2.fastq)) that contain each several 16S (V4) samples. I also have a corresponding excel file with columns “internal_sample_id”, “BarcodeName” “forwardBarcodeSequence”, “reverseBarcodeSequence”, “LibraryNumber”, “LibraryName”, “Primer”, “Region” and “Seq_ID”.

I need to have demultiplexed files (for each sample one forward and one backward fastq file). Which tool can accomplish that? I found galaxy but I couldn’t make this run on my system despite following their description online.

Would appreciate help very much!


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ok I think I need cutadapt. I read on.

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Hi @Henrik,

Im glad you solved your problem!