COV2HTML

COV2HTML visualizes NGS mapping and coverage data for prokaryotic genomes to support analysis of gene expression, transcription start sites (TSS), and genomic features.

Key Features:

• Coverage Visualization: Processes NGS mapping or coverage files to generate per-base and feature-level coverage representations highlighting genes and other genomic elements.
• Data Conversion for Large Files: Converts large mapping or coverage inputs into compact, specific coverage files that summarize information on genetic elements.
• Real-Time Analysis and Statistical Integration: Supports real-time analysis with integration of statistical results for dynamic interpretation of coverage data.
• Multi-data-type Support: Integrates and simultaneously visualizes RNA-seq and transcription start site (TSS) datasets, including stranded data.

Scientific Applications:

• Microbial genomics: Enables analysis of bacterial and phage genomes to inspect coverage, gene expression patterns, and genomic features.
• RNA-seq analysis (Campylobacter jejuni): In an RNA-seq analysis of Campylobacter jejuni, COV2HTML identified 26 of 27 genes reported in the original study.
• TSS mapping (Sulfolobus solfataricus): For stranded TSS and RNA-seq datasets from Sulfolobus solfataricus, it highlighted most transcription start sites reported in the literature.
• Regulatory element and variation inspection: Supports detection and visualization of transcription start sites and regulatory elements from coverage patterns to inform studies of genetic variation and regulation.

Methodology:

Transforms NGS mapping or coverage files into specific coverage files containing information on genetic elements and provides a visualization interface that enables real-time analysis and integration of statistical results.