Agly-Poolseq

This repository was forked from alanbergland/DEST. It contain modified scripts for mapping and quality control that were used on DEST dataset (Drosophila over Space and Time). The pipeline and Dockerfile were modified to work with Aphis glycines genome.

Metadata

populationInfo\: Has supplemental data from field populations.

PoolSeq mapping pipeline

mappingPipeline\: Contains dockerized mapping pipeline. Downloads data, produces bam files, filter files, gSYNC files

SNP calling

snpCalling\: SNP calling based on gSYNC files
SNAPE\: SNP calling based on snape output

Utility scripts

utils\: scripts for additional analyses (e.g identification of population private alleles, etc ). Some scripts were used for the analyses of soybean aphid data (e.g PNPS4VCF.py for the calculation of genome-wide $p_N$, $p_S$ and $p_N/p_S$) , some were not used. I kept these all scripts here to mirror the alanbergland/DEST original repository.

Analysis scripts

analyses\: script to reproduce the SNP-based analyses presented in the manuscript;