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I have a population in the hundreds and did an Illumina pool-seq (ended up with ~100bp reads for the whole population).

I have the reference genome for the species and now need to align all the population reads to the reference genome, figure out which are SNPs and finally determine which ones are changing from one generation to the next (about 20generations difference).

Right now I'm trying to use popoolation2 https://sourceforge.net/p/popoolation2/wiki/Main/ but it seems to be a little old as it has not been updated in ~10 years.

In Galaxy, I couldn't find any pipelines dedicated to determine population SNP variation through generation.

So two questions:

  • what software to use to determine significant variation in SNPs in a population (in poolSeq)?
  • can you suggest me a pipeline for this? if one exists.
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First focus on calling SNPs accurately. See the BWA, SAMtools, BCFtools pipeline (as described here) or GATK4 (as described here).

Once you have the [BV]CFs, then just code up the analysis to see changes over generations.

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