Trimming Illumina Seq with TRIMMOMATIC

Question

[giulia.trauzzi]

Hello,

I need to remove a common adapter and the barcode sequences from a bunch of samples (short reads - Illumina).

I was able to remove the common adapter with cutadapt from all of the samples, however I would like to know how to use trimmomatic on single end reads to remove my barcode sequences from my samples too. I need to supply a list of barcodes to the program I am assuming but I have no idea how to do this and I am struggling to find anything online.

Thanks

Giulia

[GenoMax]

Are these inline barcodes? Are they supposed to be at a fixed location (e.g. beginning of reads)?

You can use bbduk.sh with literal=sequene1,sequence2 etc. A guide is available for usage.