Contiguity

Contiguity visualizes contig adjacency and analyzes potential scaffold arrangements in de novo genome assemblies to aid resolution of ambiguous regions, particularly in bacterial genomes.

Key Features:

• Contig adjacency visualization: Displays contig adjacency information and comparisons between assembled contigs and reference sequences.
• Exploration of ambiguous regions: Represents all possible scaffold arrangements in ambiguous regions instead of collapsing them into a single scaffold, enabling inspection of alternative assemblies.
• Sequencing-agnostic adjacency graphs: Builds contig adjacency graphs independent of sequencing technology or assembler.
• Multi-source adjacency integration: Integrates read pair mappings, sequence overlaps, and De Bruijn graph exploration to maximize determination of contig adjacencies.
• Comparative-genomics enhancement: Combines adjacency evidence with comparative genomics to generate highly sensitive graphs of potential contig arrangements.
• Support for manual closure: Guides manual closure efforts in long-read sequence assemblies to improve assembly accuracy and completeness.

Scientific Applications:

• De novo bacterial genome assembly analysis: Assessing contig connectivity and potential scaffold structures in bacterial genome assemblies.
• Resolution of complex regions: Investigating unresolvable or repetitive genomic regions by enumerating alternative contig arrangements.
• Structural variant and novel sequence detection: Identifying candidate structural variants or novel sequences via alternative adjacency hypotheses.
• Comparative assembly evaluation: Contextualizing assembly adjacency hypotheses by comparison to reference sequences.

Methodology:

Constructs contig adjacency graphs by integrating read-pair mappings, sequence overlaps, De Bruijn graph exploration, and comparative genomics evidence.