verkko-fillet is an easy-to-use toolkit for cleaning Verkko assemblies. It includes tools for generating the Verkko-Fillet object, performing assembly quality checks, identifying gaps, assigning chromosomes, searching for ONT reads to help resolve gaps, filling gaps, and generating the final Rukki path (in a GAF-like format) for future Verkko CNS runs.
This Python-based implementation streamlines the entire process, starting right after the Verkko assembly is completed and preparing for the CNS run.
dependencies :
Using pip is recommended. link
The default name of the Mamba or Conda environment is verkko-fillet. If you want to use a different name, please update the name field in the environment.yaml file before proceeding.
# Generate mamba or conda env with installing dependencies.
mamba env create --file=environment.yaml
mamba activate verkko-fillet # or the name you desired
# Add python jupyter kernel
python -m ipykernel install --user --name verkko-fillet --display-name verkko-fillet
pip install verkkofillet