MeLanGE - Documentation
MeLanGE is a automated pipeline for the genomic annotation of a group of genomes, followed by the detection of the most important features to distinguish a group of genomes, as determined by a metadata label.
MeLanGE has two independent, but connected, components:
- Genome annotation
- Feature selection
MeLanGE is implemented in a Snakemake workflow, thus contributing to reproducible and scalable data analysis.
Step 0: Install conda, snakemake and ensure git
# As described in Snakemake documentation: conda install -c conda-forge mamba mamba create -c conda-forge -c bioconda -n snakemake snakemake conda activate snakemake
Step 1: Clone workflow
To use MeLanGE, you need a local copy of the workflow repository. Start by making a clone of the repository:
git clone https://github.com/sandragodinhosilva/MeLanGE.git
Step 2: Configure workflow
Configure the workflow according to your needs by editing the file
Step 3: Execute workflow
Test your configuration by performing a dry-run via
snakemake --use-conda -n
Execute the workflow locally via
snakemake --use-conda --cores N
This will run the workflow locally using
snakemake --dag | dot -Tsvg > dag.svg
After successful execution, you can create a self-contained interactive HTML report with all results via:
snakemake --report report.html
- Improve report output.
For now MeLanGE does not have a publication describing its functionalities (we are working on it). Please use a link to MeLanGE github when you reference this tool.