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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.

• 1. Data Access
• 2. Sequencing Quality Check
• 3. Demultiplexing
• 4. Filtering For Chimeric Reads
• 5. GBS Sexing
• 6. Read Processing & Mapping
• 7. 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. Phylogenetic Reconstruction
• 16. Inference of Population Splits
• 17. Measuring of Linkage Disequilibrium
• 18. GWAS

NOTE: The codes presented here were tailored to be used on our server, thus some level of adaptation is required to run these codes elsewhere.