kontiguity 0.0.1

Eukaryotic contigs retrieval and classification tool.

Kontiguity: tool for eukaryotes contigs retrieval from genomic data and classification

Kontiguity is a python and bash pipeline created to retrieve unidentified contigs from eukaryotes genomic data, and to classify said contigs based on genomic contact data (Hi-C).

Installation

pip install kontiguity

For development:

git clone https://github.com/Mae-4815162342/kontiguity.git
cd kontiguity
pip install -e .

Presenting pipeline

Kontiguity is based on a pipeline of three subfunctions:

• load which serves data retrieval and formating, and provides a scrapping method to build a dataset from DToL (ref to add).

• retrieve for the retrieval of new contigs from WGS reads aligned on a reference genome (by default produces Hi-C maps for the further step, can be deactivated).

• classify for the contigs contacts classification, based on a plasmid-detection-oriented model at this day (a larger model can be provided later.)

Those three functions can be called individually or in order with the pipeline command, which provides an option to start at any step.

Usage

Loading a dataset

kontiguity load -n Saccaromyces_cerevisiae -r S_cerevisiae.fa 

Outputs

TODO

Classification model

TODO