WGDdetector.smk

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.

Workflow

Input

• proteome (CDS and protein sequences in FASTA format)

Output

• gene families (orthomcl format)

Steps

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

Install

Clone this repository (use --recurse-submodules)

git clone --recurse-submodules https://github.com/samuelortion/WGDdetector.smk.git
cd WGDdetector

Dependencies

• Snakemake

If you want to use conda to install Snakemake, we provide a small conda environment.yaml file with a minimal set of dependencies.

Run

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.

References

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.