agtools

agtools manipulates assembly graphs in GFA format and other popular formats, enabling downstream genome and metagenome analyses through programmatic access and command-line operations.

Key Features:

• Graph Format Conversion: Converts between different assembly graph formats.
• Segment Filtering: Filters segments within assembly graphs based on specified criteria.
• Component Extraction: Extracts connected components from assembly graphs.
• Python Package Interface: Loads, queries, and analyses assembly graphs from popular genome and metagenome assemblers for integration into bioinformatics software and workflows.

Scientific Applications:

• Metagenomic Binning: Supports downstream metagenomic applications by enabling manipulation of assembly graphs constructed from metagenomic data.
• Plasmid Detection: Facilitates analysis of assembly graphs for identifying plasmid sequences.
• Viral Genome Resolution: Enables resolution of viral genomes through assembly graph manipulation.
• Haplotype Phasing: Supports phasing of haplotypes via assembly graph-based approaches.

Methodology:

agtools implements a Python framework that provides programmatic access to load, query, and analyse assembly graphs across different formats, with a command-line interface for graph format conversion, segment filtering, and component extraction.