I have genomic resequenced data for two populations of A. lyrata (6 reseq samples/population).

I also want to do different population genetics analyses. I am, aware that the sample size is small (6 haploid genomes/population) but the better part is that its the whole genome re-sequenced data. I want to find the genomic regions that 1) have mostly diverged between the two populations 2) show evidence of conservation between the population 3) show signs of extended haplotype homozygosity 4) several other population genetics test. I am also interested to do detailed fine analyses in several genomics regions (chromosome/scaffold) that have previously shown association with phenotype differences between the population.

1) Could some one advise me if the sample size of 6 haploid genomes/population would be enough to do population genetics (EHH or other if any??). If not what can/should I do to improve my inferences of population genetics statistics.

2) I have aligned the reseq data to the reference sequence, but would denovo assembly be helpful in any way to identify largely conserved vs. differentiated genomic regions between the populations. The sequence coverage is => 15x for almost all reseq data.

Any information is appreciated. Thank you in advance !