MetaCarvel

MetaCarvel reconstructs metagenomic scaffolds and detects and characterizes genomic variants within complex microbial communities.

Key Features:

• Variant-Aware Scaffolding: Incorporates a variant-aware scaffolding approach to reconstruct genomic segments and identify multiple classes of genomic variants in metagenomic data.
• Repeat Detection Strategies: Implements repeat detection strategies to distinguish repetitive sequences that complicate assembly and improve scaffold accuracy.
• Graph Analytics Integration: Leverages graph analytics to navigate assembly graphs and facilitate discovery of genomic variants.
• Coverage and Strain Resolution: Accounts for uneven depth of coverage among organisms and resolves subtle differences between nearly identical strains.
• Bambus 2 foundation: Extends scaffolding concepts from Bambus 2 to address metagenomic-specific challenges.

Scientific Applications:

• Microbial ecology: Enables reconstruction of genomes from metagenomes to inform microbial community composition and interactions.
• Evolutionary biology: Supports analysis of strain-level variation and genomic variants for evolutionary and population-genetic studies.
• Microbiome functional potential: Improves assembly-derived inference of functional potential in microbiomes through more complete and variant-aware scaffolds.

Methodology:

Requires dependencies: Python 2.7.x, Samtools, Bedtools, Networkx (version < 1.11), NumPy, and OGDF.