Aedes albopictus SNP chip

Aedes Albopictus SNP Chip Analysis

Author

Luciano V. Cosme

📧 Email: luciano.cosme@yale.edu

Overview

This repository contains the scripts and resources used for the analysis of SNP chips in the Aedes albopictus species. The work supports an extensive manuscript detailing the findings.

Contents

• File S1: WGS analyses and SNP discovery
• File S2: Mapping probes to reference genomes
• File S3: Segregation analysis from laboratory crosses
• File S4: Comparing genotypes of samples genotypes with WGS and chip
• File S5: Comparing the genotypes of replicates samples
• File S6: Functional annotation of SNPs and chip bias evaluation
• File S7: Quality control for wild samples genotyped with the chip
• File S8: Linkage analysis with PopLDdecay
• File S9: Admixture Analysis
• File S10: LEA Analysis
• File S11: fastStructure Analysis
• File S12: NeuralAdmixture Analysis
• File S13: Interpolation of admixture matrices over Asia
• File S14: Evaluating the impact of chip bias with LEA and PCA
• File S15: Fst analysis
• File S16: Create map with samples

R project with all the data is availabe in Zenodo