Hello, I am a beginner in Galaxy. I am trying to find SNP from the paired-end fastq.gz data obtained by RAD-seq. The data contains 2 parents and about 150 F2. I have already download the reference genome data.
There seem too many tools for this job, I am confused about choosing the best one and how to build a suitable workflow. Could you please tell me how to choose the tools for this job and the basic setting of them?
Thank you very much for any suggestions.