For paired end reads, an easy way of detecting adapter sequences is to try to align read pairs, and, if there is a confident enough alignment, assume the overhangs are part of the adapter sequences. With enough examples, the full adapter sequences can be recovered.
For paired end reads, an easy way of detecting adapter sequences is to try to align read pairs, and, if there is a confident enough alignment, assume the overhangs are part of the adapter sequences. With enough examples, the full adapter sequences can be recovered.