SNP calling from a scaffold.fa file

Question

[shynilasanthi]

I have assembled my illumina Rad-seq paired end short reads using Abyss. My question is, is it possible to call SNP using a reference genome for the assemblies? the output is in fasta format. Thank you in advance.

Answer 1

[pfs]

Is this what you are looking for? http://sjackman.ca/abyss-activity/

[benv]

Thanks, @pfs! I was just about to suggest the same.

[shynilasanthi]

Yes, This is exactly what I was looking for. Thank you very much!