I am using the obitools pipeline from metabarcoding.org to do dietary analysis on Illumina pair-end sequenced samples using the trnL gene. This is my first time doing a sequencing project and I hadn't given thought to the bioinformatics aspect at the time of sequencing.
My data came back demultiplexed, with each of 384 samples having the barcode in the label for forward and reverse reads. In order to use the obitools program, however, I need to have the barcode still in the sequence.
E.g. my samples look like this in the fastq file:
But I need them to look like this:
Is there a program or script that can do this? Thanks!