CPDSeqer

CPDSeqer processes and analyzes cyclobutane pyrimidine dimer (CPD) sequencing data to identify and quantify UV-induced DNA lesions at single-nucleotide resolution across genomes.

Key Features:

• High-Throughput Data Processing: Handles single-sample and multiple-sample experimental designs for both genome-wide and targeted regional analyses of CPD-Seq data.
• Quality Control: Performs quality control analyses specific to CPD-Seq experiments to assess experimental performance.
• Scalable Runtime: Typical runtime is approximately 4 hours per sample and can be accelerated through parallel computing for larger datasets.
• Diagnostic Graphics: Generates graphics to diagnose experimental performance and to identify genomic regions enriched for CPD formation.
• Comparative Analysis Scenarios: Supports three distinct analysis scenarios for comparing UV damage, enabling evaluation of directional trends and statistical significance.

Scientific Applications:

• Mutagenesis Research: Enables analysis of CPD formation and repair to investigate mechanisms of UV-induced mutagenesis.
• Cancer Genomics: Facilitates study of UV-induced DNA lesions in contexts relevant to skin cancers such as melanoma and nonmelanoma types.

Methodology:

Processes data generated by the CPD-Seq technique, accommodates various experimental designs, performs genome-wide and targeted regional analyses, and produces diagnostic graphics and reports.