This is the directory for the study on the population genetics of structural variants in the Drosophila melanogaster populations.
The goals included:
- Collecting enough long reads from NCBI SRA. Sample information needed to be clear.
- Assemble the genomes and detect SVs with the release 6 reference genome.
- Calculate basic popgen parameters, such as pi, theta, tajima's D.
- Calssify the SVs and cross-ref with their repeat contents.
- Estimate the distribution of fitness effect of various SVs and repeat types.
- Detect natural selection on specific SVs.
Validation of our SV calling pipeline by simulation is stored in another directory.
Because we were handeling noisy long reads mostly from the previous generation, we combined the results from multiple assemblers to miprove contiguity.
All the key scripts are stored under the "hpc3" folder. All the scripts are arranged by their execution order.
R scripts for visulization are in the root.
Scripts created during development are stored under "old" and "snp" folders.
Output figures for presentation and publications are under "Figure" folder.