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Pigeon Breeds Genomics | Pipeline

Filipe G. Vieira George Pacheco

Documentation outlining the pipeline's workflow.
Please, contact George Pacheco ([email protected]) should any questions arise.

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• Please navigate through the individual pages for detailed information on specific analyses.
• All scripts and downstream files are readily available from this repository.
• Be aware that the codes presented here were tailored to be used on our server, thus some level of adaptation is required when running these codes elsewhere.

• 1. Data Access
• 2. Sequencing Quality Check
• 3. Demultiplexing
• 4. Creation of Mapping Targets
• 5. Filtering For Chimeric Reads
• 6. GBS Sexing
• 7. Read Processing & Mapping
• 8. Running Stats & Filtering of Bad Samples
• 9. Filtering of Possible Paralogs
• 10. Merging of Duplicate Cases
• 11. Investigation of Filtering of Possible Paralogs
• 12. Creation of Specific Datasets
  • 12.1. Dataset I
  • 12.2. Dataset II
  • 12.3. Dataset III
• 13. Loci Information
  • 13.1. SITES
  • 13.2. SNPs
• 14. Heterozygosity Calculation
• 15. Population Genetics Statistics
• 16. Phylogenetic Reconstruction
• 17. Multidimensional Scaling
• 18. Estimation of Individual Ancestries
• 19. Inference of Population Splits
• 20. Measuring of Linkage Disequilibrium
• 21. GWAS