Snakemake port of WGDdetector pipeline, by Yang et al. 2019
WGDDetector is a pipeline for whole genome duplication (WGD) detection with genome or transcriptome annotations.
Note
The goal of this repository is to provide an implementation that matches the results given by the published pipeline while being easier to use; and to learn more doing so.
Warning
This repository is a WIP. It currently does not implement all WGDdetector steps.
- proteome (CDS and protein sequences in FASTA format)
- gene families (orthomcl format)
- gene families clustering
- large family splitting
- Ks hierarchical clustering
Clone this repository (use --recurse-submodules
)
git clone --recurse-submodules https://github.com/samuelortion/WGDdetector.smk.git
cd WGDdetector
- Snakemake
If you want to use conda to install Snakemake, we provide a small conda environment.yaml
file with a minimal set of dependencies.
Example command line:
snakemake --cores 1 --snakefile ./workflow/Snakefile --use-conda
A small wrapper on the snakemake CLI is provided in cli.py
, to offer a similar interface and option as the original WGDdetector, with the drawbacks of being less versatile.
Example of cli adapted from wgddetector/example/00.run.sh
:
python3 cli.py --input_cds test.cds.fa --input_pep test.pep.fa --output_dir output --tmp_dir tmp --thread_num 4 --cluster_engine mmseqs2
We rather recommend to use the snakemake
CLI.
Yang Y, Li Y, Chen Q, Sun Y, Lu Z: WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations. BMC Bioinformatics 2019, 20(1):75.