Genomic analysis of host specific fungal pathogen Pneumocystis to mammals
├── LICENSE
├── README.md <- The top-level README for developers using this project.
├── data
│ ├── external <- Data from third party sources.
│ ├── interim <- Intermediate data that has been transformed.
│ ├── processed <- The final, canonical data sets for modeling.
│ └── raw <- The original, immutable data dump.
│
├── docs <- Mostly figures
│
├── notebooks <- Jupyter notebooks. Naming convention is a number (for ordering),
│ the creator's initials, and a short `-` delimited description, e.g.
│ `1.0-jqp-initial-data-exploration`.
│
│
├── reports <- Generated analysis as HTML, PDF, LaTeX, etc.
│ └── figures <- Generated graphics and figures to be used in reporting
│
├── requirements.txt <- The requirements file for reproducing the analysis environment, e.g.
│ generated with `pip freeze > requirements.txt`
│
├── src <- Source code for use in this project.
│ ├── data <- Scripts to download or generate data
| <- Pwk.sm (Pneumocystis wakefieldiae genome assembly notes - snakemake format)
| | <- Pcan.sh (Pneumocystis canis genome assembly notes)
| | <- Pmac.sh (Pneumocystis macacae genome assembly notes)
│ |── envs
│ │
│ └── visualization <- Scripts to create exploratory and results oriented visualizations (R )
Data description (selected):
Pipelines:
src/data/intra_inter_div.smk: whole genome pairwise divergence computation (snakemake)
src/data/Pmac.sh: Pneumocystis macacae wgs assembly (bash)
src/data/Pwk.smk: Pneumocystis wakefieldiae assembly (snakemake)
src/data/Pcan.sh: Pneumocystis canis assembly (bash)
Datasets:
docs/inter_intra_div/scores.csv: whole genome pairwise divergence scores