clouded apollo genomics.

This is a dedicated repository for the conservation genomics of Clouded apollo butterfly.

Maaping to the Reference genome.

Apollo_stampy.py is a python script that writes sbatch scripts. These scripts were submitted to uppmax to get our final bam files.

SNP calling

SNP calling was performed on all bam files using BCFtools.

bcftoolsCommand=mpileup --threads 10 --skip-indels -Ou -f /scratch/vt20265/clouded_apollo/Genome/GCA_907164705.1_Parnassius_apollo_genomic.fasta /scratch/vt20265/clouded_apollo/mapping/S121.bam /scratch/vt20265/clouded_apollo/mapping/S122.bam /scratch/vt20265/clouded_apollo/mapping/S123.bam /scratch/vt20265/clouded_apollo/mapping/S124.bam /scratch/vt20265/clouded_apollo/mapping/S125.bam /scratch/vt20265/clouded_apollo/mapping/S126.bam /scratch/vt20265/clouded_apollo/mapping/S127.bam /scratch/vt20265/clouded_apollo/mapping/S128.bam /scratch/vt20265/clouded_apollo/mapping/S129.bam /scratch/vt20265/clouded_apollo/mapping/S130.bam /scratch/vt20265/clouded_apollo/mapping/S131.bam /scratch/vt20265/clouded_apollo/mapping/S132.bam /scratch/vt20265/clouded_apollo/mapping/S133.bam /scratch/vt20265/clouded_apollo/mapping/S134.bam /scratch/vt20265/clouded_apollo/mapping/S135.bam /scratch/vt20265/clouded_apollo/mapping/S136.bam /scratch/vt20265/clouded_apollo/mapping/S137.bam /scratch/vt20265/clouded_apollo/mapping/S138.bam /scratch/vt20265/clouded_apollo/mapping/S139.bam /scratch/vt20265/clouded_apollo/mapping/S140.bam /scratch/vt20265/clouded_apollo/mapping/S141.bam /scratch/vt20265/clouded_apollo/mapping/S142.bam /scratch/vt20265/clouded_apollo/mapping/S143.bam /scratch/vt20265/clouded_apollo/mapping/S144.bam /scratch/vt20265/clouded_apollo/mapping/S145.bam /scratch/vt20265/clouded_apollo/mapping/S146.bam /scratch/vt20265/clouded_apollo/mapping/S147.bam /scratch/vt20265/clouded_apollo/mapping/S148.bam /scratch/vt20265/clouded_apollo/mapping/S149.bam /scratch/vt20265/clouded_apollo/mapping/S151.bam /scratch/vt20265/clouded_apollo/mapping/S152.bam /scratch/vt20265/clouded_apollo/mapping/S153.bam /scratch/vt20265/clouded_apollo/mapping/S154.bam /scratch/vt20265/clouded_apollo/mapping/S155.bam /scratch/vt20265/clouded_apollo/mapping/S156.bam /scratch/vt20265/clouded_apollo/mapping/S157.bam /scratch/vt20265/clouded_apollo/mapping/S158.bam /scratch/vt20265/clouded_apollo/mapping/S159.bam

PCA

The code used to generate the PCA was provided in Clouded_apolo_PCA.R

LEA/Admixture

The code used to perform admiture using LEA was provided in LEA_clouded_apollo.R

IBD (Identity by descent) analysis and Plots

IBD analysis and dendrogram was also provided in Clouded_apolo_PCA.R

FST

Clouded_Apollo_FST_dxy.py extimates the Fst, Dxy, fixed, private and shared polymorphisms.