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de novo SNP development from pool seq

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

snp donovo no refernce genome
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updated by GenoMax GenoMax • written by Phismil • Phismil

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.

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written by Brian Bushnell Brian Bushnell

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?

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written by Fabio Marroni Fabio Marroni

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

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written by Phismil • Phismil

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.

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written by Fabio Marroni Fabio Marroni

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

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written by Phismil • Phismil

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