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Old 09-23-2015, 12:40 PM   #4
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
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I think if there is flexibility, then I would genotype 10 individuals from each population in 2 lanes of sequencing, 95 individuals per lane. You can re-use the same adapters in each of the two lanes, of course, so the extra cost of making the libraries should be easily offset by the cost of the third lane that is no longer needed.

You'd end up with solid genotypes of 20 chromosomes per population (are you sequencing diploids?), giving a pretty accurate estimate of allele frequency at 5% resolution from each site.
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