Pool-seq Nextera or Truseq

[fraca]

Hi to all,
This is my first post and I'm new to NGS world, I found this forum very interesting and useful.
For my PhD I have to do a GWAS study on Arabidopsis lyrata. I have about 50 population (25 individual per pop) and I want to find the correlation between the climatic variable and the SNPs.

The approch that I would like to use is pooled whole genome resequencing. Pooling the individuals of one population, making one library for each population and sequencing that on Hiseq. Finally get the population alleles frequencies.
For making the library there are two kits Nextera and Truseq. I prefer to use the Nextera because need less DNA, it is used for resequencing studies and the protocol is easy, fast and cheap compare to Truseq.

Has someone use the Nextera kit for sequencing pooled sample?


thanks

[SNPsaurus]

Sure, Nextera works fine for a pooled population. Since you want to estimate the population allele frequency, don't skimp on the input amount and keep the number of PCR cycles down. You may have some issues calling alleles that are present in a single heterozygous individual, since that would be at a 2% frequency. So some extra quality filtering might be needed to avoid sequencing errors showing up at that frequency.

[fraca]

Thanks SNPsaurus