Snp Marker Development Using Rad Sequencing

Question

[vaibhavbarot]

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.

[cpcantalapiedra]

I can't give you any details, since a don't know much about the topic, sincerely. Just wanted to comment to suggest that maybe you could use a GBS based pipeline as well, that maybe are more popular today and easy to find out there. Anyway, the pipeline could change a lot depending on the plant genome that you would use. It is not the same to work with Arabidopsis, rice or barley current genomes. However, at least with GBS, you could work with this kind of data even without a reference, maybe first defining a set of tags as reference, that maybe you could construct with some k-mer clustering algorithm, and then mapping you sequence tags to those references with for example BWA or Bowtie2. Then you maybe could start with the common SNP calling pipelines, like mpileup, GATK, atlasSNP, FreeBayes, I don't know.

Answer 1

[zam.iqbal.genome]

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

[zam.iqbal.genome]

I should have said - this basically combines STACKS and Cortex.