PACMAN

PACMAN analyzes and visualizes DNA methylation patterns from PacBio sequencing to generate Circos-based representations of methylated motif counts, locations, and non-methylated regions across one or both DNA strands.

Key Features:

• Implementation: Implemented in Perl.
• Data input: Accepts a bacterial full or draft genome in FASTA format and motifs data from PacBio sequencing analysis in GFF format.
• Visualization (Circos): Generates publication-quality Circos images depicting distribution and frequency of methylated motifs and non-methylated regions across one or both DNA strands.
• IPDratio: Adjusts modification calls based on the IPD ratio.
• Coverage: Filters motif calls by sequencing coverage levels.
• Identification Quality Value (idqv): Filters motifs by identification quality value to prioritize high-confidence calls.

Scientific Applications:

• Methylation mapping in bacterial genomes: Visualizes and summarizes DNA methylation patterns across bacterial full or draft genomes.
• Methylated motif quantification: Reports counts and locations of methylated motifs derived from PacBio GFF motif calls.
• Non-methylated region identification: Identifies and displays non-methylated regions on one or both strands for comparative analysis.
• Quality-filtered modification analysis: Enables selection of modification calls using IPDratio, coverage, and idqv thresholds for downstream interpretation.

Methodology:

Implemented in Perl and using Circos for image generation; accepts FASTA genomes and PacBio-derived GFF motif files and applies IPDratio, coverage, and identification quality value (idqv) filters.