Finding polymorphic SSR among different transcriptome assemblies

[setar...@gmail.com]

Hi all,

I'm working on a de novo transcriptome assembly. Could you please kindly tell me if lobSTR is a suitable tool for finding polymorphic SSRs among assembled transcriptome?

Any alternative tool for this purpose?

Thanks in advance

[Melissa Gymrek]

Hello,

lobSTR (and more recently, HipSTR (https://github.com/tfwillems/HipSTR) which I suggest you use instead) is meant to work on short reads, not on assembled genomes or transcriptomes. If you have the short reads, you could theoretically run HipSTR on those but we haven't tried that out ourselves.

Best,

~Melissa

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