Metadata-Version: 2.2
Name: verkkofillet
Version: 0.1.4
Summary: verkko fillet pkg
Author-email: Juhyun Kim <kimj75@nih.gov>
Maintainer-email: Juhyun Kim <kimj75@nih.gov>
License: Copyright (c) 2018 The Python Packaging Authority
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/jjuhyunkim/verkko-fillet
Project-URL: Issues, https://github.com/jjuhyunkim/verkko-fillet/issues
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE

# verkko-fillet : post verkko graph and assembly cleaning in Python

verkko-fillet is an easy-to-use toolkit for cleaning [Verkko](https://github.com/marbl/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.


### Installation

dependencies : 
* [gfacpp](https://github.com/snurk/gfacpp)

Using `pip` is recommended. [link](https://pypi.org/project/verkkofillet/)


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
```
