biosyntheticSPAdes

biosyntheticSPAdes reconstructs biosynthetic gene clusters (BGCs) from fragmented genomic and shotgun metagenomic assemblies to improve recovery of pathways relevant to antibiotic and natural product discovery.

Key Features:

• Fragmented Assembly Handling: Manages assemblies where BGCs are dispersed across multiple contigs rather than assuming each BGC is contained within a single contig.
• Genome Assembly Graph Utilization: Leverages genome assembly graphs to infer connections between contigs and reconstruct longer BGC-encoding segments.
• Application in Metagenomics: Improves BGC recovery from shotgun metagenomic datasets with short contigs by enabling reconstruction across contigs.

Scientific Applications:

• Antibiotic Discovery: Supports identification and characterization of BGCs encoding antibiotic compounds by enabling more complete reconstructions.
• Natural Product Research: Facilitates exploration of genetic pathways for biosynthesis of natural products by reconstructing multipart BGCs from fragmented data.

Methodology:

Analyzes assembly graphs derived from genomic and metagenomic data, identifies potential connections between contigs that may encode parts of a single BGC, and combines those contigs into longer segments.