MetaCortex

MetaCortex reconstructs assemblies from metagenomic sequencing data and captures intra-species diversity, including viral haplotypes and bacterial strain-level variation, by identifying local variation in assembly graphs.

Key Features:

• Local variation detection: Identifies local variations along assembled sequences within the underlying assembly graph to capture intra-species diversity.
• Signature-based representation: Focuses on signatures of local variation to represent haplotypes and strain-level variants within populations.
• Sequence graph output: Outputs assemblies in sequence graph format that encode alternative local variants and structural diversity.
• Enhanced assembly metrics: Demonstrates improved genome coverage and contiguity relative to other metagenomic assemblers.

Scientific Applications:

• Microbial ecology: Characterizes strain-level diversity within complex microbial communities.
• Evolutionary biology: Represents intra-species variation and haplotypes to study evolutionary dynamics.
• Pathogen genomics: Resolves viral haplotypes and bacterial strain variation in pathogen and viral community samples.
• Benchmarking and validation: Validated on mock viral communities with high strain-level diversity and on simulated communities containing various strains, showing improved coverage and contiguity compared with other assemblers.

Methodology:

Identifies local variations along assembled sequences within the assembly graph, focuses on signatures of local variation, and outputs assemblies in sequence graph format.