Usage Principles

Usage Principles#

Import verkko-fillet as :

import verkkofillet as vf

How to use#

The verkkofillet module, abbreviated as vf, consists of three sub-modules: pp, tl, and pl.

  • vf.tl: Provides tools for running shell scripts.

  • vf.pp: Includes modules for preprocessing and modifying datasets.

  • vf.pl: Dedicated to plotting and visualization.

The typical workflow consists of subsequent calls of data analysis tools in vf.tl, e.g.:

vf.tl.getT2T(obj, **tool_params)

where obj is an verkko-fillet object.

Verkko-fillet object#

verkkofilletobj verkko-fillet is based on the verkko-fillet object, which collects relevant files and stores them within the object itself. Various sub-attributes, such as .gaps, .stats, and others, are stored as Pandas DataFrames, allowing users to flexibly analyze the data and save it separately to local storage if needed.

The available attributes are as follows:

  • .verkkoDir: Directory containing the verkko results.

  • .verkko_fillet_dir: Output directory for verkko-fillet results.

  • .paths: Path file extracted from assembly.paths.tsv.

  • .version: Genome version.

  • .species: Genome species.

  • .stats: Assembly statistics (e.g., contig and chromosome information, completeness).

  • .gaps: Gap information extracted from the .path file.

  • .gaf: Graph alignment results (GAF format).

  • .qv: Quality value (QV) calculation results using meryl and merqury.

  • .history: Log of all modifications made during the gap-filling process.

  • .scfmap: Assembly scaffold mapping file (assembly.scfmap).

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