I've got a bit of a weird result with some reads I've simulated. I've used BBMaps' randomreads.sh to simulate some illumina paired end reads, and as I'm playing around with introducing errors I decided to run FastQC and multiQC on the data. Weirdly, my reads are showing a large amount of illumina universal adaptor on the 3' end of the reads, yet I haven't added any in at any stage. I've searched randomreads.sh' docs and it doesn't seem to add anything in automatically, and so I'm left pondering where these adaptors have come from.
Does anyone know if randomreads.sh adds any in automatically during simulation? Or is there a chance the reference genome from which I'm simulating the reads contains adaptors and that's where they're coming from? The reference is very high quality and was put together by the IWGSC so I doubt it, but you never know I guess. Or is there a chance this is a false positive hit by FastQC?
Any insight is greatly appreciated.