P.chondrillina-project-scripts

The command lines and programming script used in this project are divided into three parts (folders):

Part 1: Genome assembly & SNPs calling:

The file 'Genome assembly' contains the command lines used in Genome assembly, polishing and quality control.

The file 'SNPs calling' contains the command lines used in mapping, PCR duplicates removal, SNPs calling, SNPs quality filtering, SNPs counting.

Part 2: population structure

The file 'ADMIXTURE for admixture analysis' contains the command lines used in admixture analysis with software ADMIXTURE and result visualization.

The file 'IQTREE2 for phylogenomic tree' contains the command lines used in phylogenomic analysis with software IQTREE2.

The R script 'PCoA&DAPC.R' is for Principal Coordinates Analysis and Discriminant analysis of principal components with R package adegenet.

Part 3: genome scans

The file 'Fst&Tajima'sD' contains command lines used to calculate Fst and Tajima'sD using VCFtools

The file 'Divide SNPs into contigs' contains command lines used to divide genome-wide SNPs into contigs in order to calculate pi and Dxy with the R package Popgenome.

The R script 'pi&Dxy.R' is for calculating pi and Dxy statistics with R package Popgenome.

The R script 'visualization.R' is for merging all the statistic results (pi, Dxy, Fst, Tajima'sD) into a data frame and visualizing the results.