Can someone help me with analysing raw ddRAD sequence data ?

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Abhijeet Singh

It might (most probably) not possible to use a single software for A-Z analysis

User-friendliness would depend on the understanding of the concept by the user and how the analysis is carried out with any software. It is not a universal thing.

Have you tried this Stacks 2?

Rochette, NC, Rivera‐Colón, AG, Catchen, JM. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Mol Ecol. 2019; 28: 4737– 4754. https://doi.org/10.1111/mec.15253

Aswathi A.P

Thank you very much for the answer. Regarding Stacks,I have just read about it but haven't tried yet. I will definitely look into the paper.

Thanks

Martin Schwentner

Stacks is a good option. I personally prefer ipyrad (https://ipyrad.readthedocs.io/en/latest/) which is a bit easier to handle in my opinion.

Thank you very much for the suggestion Martin Schwentner.Actually, I haven't heard about ipyrad before,so I will definitely check it out.