I am interested in finding SSR markers in our recently sequenced plant genome. Our plant genome is non-model and it is tetraploid. It was sequenced in hiseq2000 of one paired-end library of 101bp length.
We have denovo assembled genome using soapdenovo. The coverage of genome is around 5X. Is it possible to get reasonable SSR by using genome-wide identification by using tools like MISA (Microsatellite identification; http://pgrc.ipk-gatersleben.de/misa/)?.
Any good tool to find SSR and for primer design appreciated?
We have denovo assembled genome using soapdenovo. The coverage of genome is around 5X. Is it possible to get reasonable SSR by using genome-wide identification by using tools like MISA (Microsatellite identification; http://pgrc.ipk-gatersleben.de/misa/)?.
Any good tool to find SSR and for primer design appreciated?
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