Hi, I have paired-end fastq file which contain the sequences of the target regions along with probes sequences on either side (in entirety or partially). I have sequences of all the 3,200 probes. I want to quickly trim the probe sequences from the fastq files if they occur on either side of the target region (only if they start with or end with the probes).
Does anyone have a suggestion for a tool to do the above? I have tried Trimmomatic and Cutadapt but they are too slow as they are designed with only a handful of probes (or adapters) in mind?
Is there anyway to remove 1000's of probes that occur at the end of the reads in paired-end fastq files? Thanks!