Hi I am new to RAD tag sequencing.
I want to set up SNP marker development pipeline using RAD sequencing for Plant Genome data.
Could any one guide for tools required to set pipeline in detail?
Thanks in advance.
It depends a little on whether your plant species has a reference genome, and the ploidy. I'm no expert on this, but this paper (I am an author) offers a solution for species where you do NOT have a reference genome, and you want to build SNP markers without the expense of building a reference:
Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data. Senn H, Ogden R, Cezard T, Gharbi K, Iqbal Z, Johnson E, Kamps-Hughes N, Rosell F, McEwing R. Mol Ecol. 2013 Jun;22(11):3141-50. doi: 10.1111/mec.12242