mashphage genomes.fa.gz
The goal of mashphage is to provide a mean to rapidly and accurately cluster (actino) bacteriophage genome
in know clusters. Mashphage comes bundled with a genomic signature of actinobacteriophage genomes, which enables
to fastly and accurately assign actinobacteriophages genomes in the known cluster schemes.
However, the user can specify a custom path (with -d option) to a genomic signature created using sourmash sketch.
First install sourmash:
conda install -c conda-forge -c bioconda sourmash
# alternatively you can do
pip install sourmashAnd install mashphage from pypi:
pip install mashphage# Download ConoDictor development version
git clone https://github.com/Ebedthan/mashphage mashphage
# Navigate to directory
cd mashphage
# Install with poetry: see https://python-poetry.org
poetry install --no-dev
# Enter the Python virtual environment with
poetry shell
# Test mashphage is correctly installed
mashphage -hIf you do not want to go into the virtual environment just do:
poetry run mashphage -hSubmit problems or requests to the Issue Tracker.