Phigaro

Phigaro detects and annotates prophage regions in genome and metagenome assemblies to enable high-throughput prophage sequence analysis.

Key Features:

• Prophage detection: Detects prophage regions within raw genome and metagenome assemblies.
• Prophage annotation: Produces systematic annotations for identified prophage regions.
• Prophage genome maps: Generates dynamic annotated prophage genome maps that visualize prophage structures.
• Transposon insertion site identification: Identifies potential transposon insertion sites within prophages.
• High-throughput processing: Supports analysis of large-scale metagenomic datasets.
• Input support: Processes raw input from genome assemblies and metagenomic datasets.
• Implementation: Implemented in Python.

Scientific Applications:

• Microbial community analysis: Characterizes prophage content within complex metagenomic datasets to study community composition.
• Bacterial evolution: Illuminates roles of prophages in bacterial evolution and genomic variability.
• Horizontal gene transfer: Assesses prophage-mediated horizontal gene transfer and its impact on bacterial genomes.
• Pathogenicity and ecology: Investigates contributions of prophages to bacterial pathogenicity and ecological interactions.
• Genomic rearrangements: Maps potential transposon insertion sites to study genomic rearrangements and adaptation.

Methodology:

Processes raw genome and metagenomic assemblies to identify and annotate prophage regions, generate annotated prophage genome maps, and mark potential transposon insertion sites.