I would like to trim/mark adapters using trimmomatic or picard MarkIlluminaAdapters from a series of Illumina Paired-End read fastqs. The fastq files may have been done using different kits or different generations/versions of illumina chips.
Without knowing ahead of time how the libraries were prepared (or which kit was used), Is there a safe "catch all" adapter sequence (or set of such sequences) that can be passed to a trimming tool and that would cover all Illumina kits? In other words, what are we expected to know about the fastq to ensure correct trimming?
edit: Picard defines a few built-in adapters which cover many standard kits, but it's not immediately obvious if you need to pass a common one (built-in sequences defined here).