Speciation & Population Genomics: a how-to-guide
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Learning Unix
- Getting used to Unix
- Going further with Unix
- awk tutorial
Handling NGS data
- Understanding NGS data
- Filtering reads
- Mapping to a reference genome
- Variant calling
- Filtering and handling VCFs
- Checking for PCR duplication problems, contamination, etc.
Learning R
- Introduction to R
- Data manipulation and visualisation in R
- More advanced R
Population structure
- Using PCA
- Detecting structure with ADMIXTURE
- Detecting hybridization with Dstats
- Detecting hybridization with treemix
Genome scans
- Calculating LD decay
- Computing per site Fst
- Sliding window differentiation, variance and introgression
- Statistical phasing with shapeit2
- Identifying selection with haplotype statistics
- Identifying candidate genes
Demographic inference
- Estimating the site-frequency-spectrum
- Demographic modeling with fastsimcoal2
Extra material
- Comparative genomics with Orthofinder
- Simulating data with SliM
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