| SNiPloid
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Preprocess your data using 
SNiPloid assumes that short reads datasets (i.e. samples) derived from distinct accessions (diploid or polyploid) have been separately preprocessed as described here.
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Run SNiPloid to compare SNPs between accessions.
SNiPloid compares SNPs in overlapping user-defined interval
Run SNiPloid on-line or
Download SNiPloid executable
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Exploit SNiPloid results
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