GenAPI

GenAPI performs gene presence-absence analysis across fragmented bacterial genome assemblies to identify gene loss and acquisition events resulting from short-read sequencing technologies.

Key Features:

• Fragmented Genome Assembly Analysis: Accounts for genes that are partially assembled or split across multiple contigs in short-read–derived assemblies.
• High Sensitivity and Precision: Demonstrated high sensitivity and maintained precision in detecting presence-absence events on simulated and real datasets.
• Comparative Performance: Outperformed six evaluated gene presence-absence tools on fragmented genome assemblies while showing comparable precision and recall on complete genomes.

Scientific Applications:

• Bacterial evolution and adaptation: Enables study of gene loss and acquisition underlying bacterial evolutionary and adaptive processes.
• Virulence: Identifies presence-absence of virulence-associated genes to investigate changes in pathogenic potential.
• Antibiotic Resistance: Tracks gain and loss of antibiotic resistance genes to monitor resistance spread and emergence.
• Metabolic Capability: Detects variation in metabolic genes to assess changes in metabolic pathways relevant to biotechnology and ecology.

Methodology:

Compares gene content across multiple bacterial assemblies and employs algorithms sensitive to partial or split gene assemblies to detect presence-absence events.