Question

SNP calling from a scaffold.fa file

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4.8 years ago

shynilasanthi ▴ 40

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.

abyss SNP calling fasta • 1.7k views

ADD COMMENT • link updated 4.8 years ago by pfs ▴ 280 • written 4.8 years ago by shynilasanthi ▴ 40

score 4 · Answer 1 · 2017-12-07

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4.8 years ago

pfs ▴ 280

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

ADD COMMENT • link 4.8 years ago by pfs ▴ 280

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

ADD REPLY • link 4.8 years ago by benv ▴ 720

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

ADD REPLY • link 4.8 years ago by shynilasanthi ▴ 40