This repository contains bash command lines and scripts used in the population genomics analysis of Ellobium Chinense to obtain SNPs dataset, summarize sequencing statistics, calculate Fixation index, perform principal component analysis, and estimate demographic history using Multiple Sequentially Markovian Coalescent model.
We describe detailed parameters from obtaining SNPs dataset to principal component analysis in Ellobium_data_processing_popgen_analysis.txt, and detailed parameters of MSMC2 in Ellobium_MSMC2.txt.
The methods and software are stated in the section of Methods-Population genomic analysis and References.