I have a fastq file with merged amplicon sequence reads post Illumina sequencing. However, the library was build by ligating the Illumina adapters to the amplicon. Therefore, the merged amplicon sequences have no common direction. Now I had the idea to use a script that finds the exact sequence of a certain primer and reverse complements those sequences within the fastq file. One _is_ able to do this in Geneious, however, I'd rather like to use a script/tool to incorporate into the pipeline I want to establish. I already looked into BBtools and others, however, couldn't find a tool doing this.
Thank you for any input.