de novo SNP development from pool seq

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6.7 years ago

Phismil ▴ 20

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 • 1.8k views

ADD COMMENT • link updated 6.7 years ago by GenoMax 141k • written 6.7 years ago by Phismil ▴ 20

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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 REPLY • link 6.7 years ago by Brian Bushnell 20k

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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 REPLY • link 6.7 years ago by Fabio Marroni ★ 3.0k

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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 REPLY • link 6.7 years ago by Phismil ▴ 20

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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.