Question: de novo SNP development from pool seq
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gravatar for Arsalan
2.3 years ago by
Arsalan10
Arsalan10 wrote:

Dear colleagues, I am wondering if you have any suggestions regarding the best package/practice for de novo SNP development from pool seq data? The species that I am working on does not have reference genome available. Many thanks in advance

donovo snp no refernce genome • 926 views
ADD COMMENTlink modified 2.3 years ago by genomax74k • written 2.3 years ago by Arsalan10
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Sounds like the first thing you need to do is assemble it and annotate the assembly with genes. PacBio data can yield some very nice assemblies.

ADD REPLYlink written 2.3 years ago by Brian Bushnell16k
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What do you mean by pool seq data? Did you amplify one region of the genome and sequence it in a large number of pooled subjects? Are you interested in genome-wide SNPs or SNPs in a selected region?

ADD REPLYlink written 2.3 years ago by Fabio Marroni2.4k

Thanks Fabio ! My data are genome-wide RAD seq data from several pools.I don't have reference genome for the studied animals. I appreciate your suggestions. cheers

ADD REPLYlink written 2.3 years ago by Arsalan10
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Mmmm... then I suggest you give a look to stacks. It is a widely used software for analyzing RAD-seq data. HAving RADseq, you can "easily" assemble the small loci using stacks. The manual explains how to do that. I am not sure on how to best manage pooled data, I never had to do that with stacks.

ADD REPLYlink written 2.3 years ago by Fabio Marroni2.4k

Thanks Fabio , Yes I use to use Stack. It is an excellent package.

ADD REPLYlink written 2.3 years ago by Arsalan10
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