can anyone give some example codes to remove primer sequence from MiSeq PCR amplicon sequences

Question

[yiangulo]

Hi,

I have some illumina MiSeq paired end sequence data to process. the data are from PCR samples and I need to remove the primer sequences before processing further, including phylogenetic tree analysis. I am completely new in bioinformatics, so the question might seem very basic. I would like to know how to trim out the primer sequences from the read, and at what step this trimming can be used?

Thanks

Answer 1

[a.a.kechin]

Try cutPrimers that does it: https://github.com/aakechin/cutPrimers. For some question, you can write me or on the github page