I have a two adapter trimmed Illumina fastq files (read1 and read2). I would like to identify the primer sequence. I have some idea what the primer sequences are however, they appears to be degenerate. So far I've found over 200 variations for the primer sequence in reads and looking for a tool that would group them and produce degenerate primer sequence.
Next, I plan to separate the reads into separate files based on the primer sequence using bbtools.
Please suggest an approach/tool to use.