Can I map SNPs without a reference genome?

Question

[caromimo]

I have a list of SNPs from a species that has yet to be sequenced (i.e. no reference genome). The closest relevant available genome is from another species in the same Order.

Is physical mapping of the SNPs possible based on this information?

Are there Python tools available to do this?

Thank you.

[Sam]

What are you trying to do? How do you get the Snps in the first place if you don't have the reference genome?

Are you trying to ask: 1. We have some candidate genes on a species that doesn't have a reference genome. What is the possible way for us to identify the Snps?

If that's what you are asking, you might have to perform some kind of denovo assembly, or if you have a species whose genome is very similar to the one you are studying, you might try to use that as a proxy

[GouthamAtla]

You can get SNPs with out reference genome. These workflows are generally available for RAD-Seq or ddRAD-Seq protocols.

A few pipelines are :

• http://creskolab.uoregon.edu/stacks/
• http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0/pyRAD_v.3.0.ipynb

[GouthamAtla]

Do you have some common information between the SNP file and the closest genome?