panISa

panISa detects insertion sequences (IS) in bacterial genomes from next-generation sequencing (NGS) resequencing BAM files to identify IS insertion events for studies of bacterial genome evolution and adaptation.

Key Features:

• BAM-format resequencing input: Operates on NGS resequencing data provided as BAM files.
• Ab initio / database-free detection: Identifies ISs directly from sequencing reads without requiring a pre-existing IS database.
• Clipped reads analysis: Detects IS insertions by counting clipped reads at the start and end positions of candidate insertion sites.
• Direct repeat overlap detection: Uses overlap of clipped reads with direct repeats as evidence for IS insertion events.
• Inverted repeat reconstruction (IRL/IRR): Reconstructs beginning regions on both sides of suspected ISs to search for inverted repeat structures.
• ISFinder validation: Validates detected events through nucleotide sequence similarity comparisons with the ISFinder database.

Scientific Applications:

• Evolutionary studies of bacterial pathogens: Reanalysis of published outbreak datasets to characterize IS-driven genome evolution in species such as Acinetobacter baumannii, Vibrio cholerae, and Enterococcus faecalis.
• Phylogenetic consistency assessment: Comparison of IS distribution patterns with SNP-based phylogenetic trees to support evolutionary inferences.
• Investigation of pathogen adaptation and resistance: Identification of IS-related events, including insertions upstream of the ampC gene in cephalosporin-resistant isolates and insertions within pathogenicity islands.

Methodology:

Processes NGS resequencing BAM files by aligning reads against reference genomes, applies an ab initio detection algorithm to identify IS insertions from clipped read patterns and inverted repeat (IRL/IRR) structures, automatically curates detected events, and validates candidates via nucleotide sequence similarity comparisons with the ISFinder database.