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.

• proteome (CDS and protein sequences in FASTA format)

• gene families (orthomcl format)

1. gene families clustering
2. large family splitting
3. 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.