Genofunc

Genofunc annotates and extracts genomic features from viral whole-genome sequences to produce aligned and annotated datasets for downstream phylogenetic and epidemiological analyses.

Key Features:

• Command-line functions: A suite of command-line tools to process raw viral genome sequences into aligned and annotated data.
• Genome annotation and feature extraction: Functions for annotating viral genomes and extracting key genomic features from large datasets.
• Pipeline integration: Compatibility with workflow managers Snakemake and Nextflow for incorporation into automated pipelines.
• Implementation: Implemented in Python.

Scientific Applications:

• Viral genomics: Generation of annotated sequence datasets to support analyses of viral diversity and genome organization.
• Phylogenetics: Preparation of aligned and annotated data for downstream phylogenetic analyses to track transmission and mutation patterns.
• Epidemiology and outbreak investigation: Processing of pathogen genomes to support analyses used during epidemics and outbreaks.

Methodology:

Developed for a large-scale HIV sequencing project and benchmarked against annotated sequence gene coordinates from the Los Alamos HIV database; validation showed downstream phylogenetic analysis results comparable to reported literature.