I am processing single-end illumina reads coming from a PCR library.
I know the flanking sequences of my reads and need to:
- select the sequence that contain the 5' constant region (with >90%homology for the 39 first nt; 100% for the last 3nt) and remove that sequence
- remove the 3' constant sequence when it is present
All the tools I found do not offer mismatches/gaps parameters, or can not be inserted in a workflow.
Do you know what tools I can use to do that ? (I used to do it with flexbar but it cannot be integrated into workflows),
Thanks for your help !