Selscape
selscape is a flexible workflow framework designed to study patterns of natural selection across different species. It integrates different detection methods such as betascan to detect long-term balancing selection, selscan for positive selection and dadi-cli for distribution of fitness effects (DFE). In addition, to understand biological functions of selected candidates, annotation with ANNOVAR and functional enrichment with Gowinda are performed.
Key Features
selscape is designed for flexibility and supports:
| Feature | Description |
|---|---|
| Multi-species support | Configurable for any species through YAML files |
| Selection methods | betascan, selscan, dadi-cli integration |
| Flexible data input | Customizable VCF file naming and chromosome schemes |
| Functional analysis | Gene annotation and GO enrichment |
| Scalable execution | Snakemake workflow with cluster support |
Requirements
selscape works on Linux operating systems with the following dependencies:
- bcftools=1.21
- bedtools=2.31.1
- bioconductor-biomart=2.62.0
- cyvcf2=0.31.0
- dadi=2.3.0
- dadi-cli=0.9.1
- matplotlib=3.9.4
- nlopt=2.7.1
- numpy=1.26.4
- pandas=2.2.3
- pip=25.0.1
- plink=1.90b6.21
- pyliftover=0.4.1
- pysam=0.23.0
- python=3.11.13
- r-base=4.4.3
- r-ggplot2=3.5.2
- r-qqman=0.1.9
- r-readr=2.1.5
- scipy=1.13.1
- snakemake=7.32.4
Installation
Users can install selscape using the following steps:
-
Install Mambaforge (if not already installed): Mambaforge installation guide
-
Clone the repository:
git clone https://github.com/xin-huang/selscape.git
cd selscape
- Create and activate the environment:
mamba env create -f workflow/envs/env.yaml
mmaba activate selscape
Users should manually download ANNOVAR and place it in resources/tools. An institutional email adress is required for registration.
Help
For detailed configuration and usage instructions, see the documentation. If you need further help, such as reporting a bug or suggesting a feature, please open an issue.