ampliMethProfiler

ampliMethProfiler performs epihaplotype-based analysis of CpG methylation from targeted deep bisulfite sequencing amplicons to characterize single-molecule methylation patterns.

Key Features:

• Epihaplotype analysis: Extracts and characterizes combinations of methylated and unmethylated states across CpG sites within individual DNA molecules.
• Targeted deep bisulfite sequencing support: Processes amplicon reads derived from targeted deep bisulfite sequencing for high-resolution methylation profiling.
• Single-molecule profiling: Reports single-molecule CpG methylation profiles rather than only aggregate methylation levels.
• Statistical tools integration: Includes statistical methods to analyze and interpret complex epihaplotype compositions.
• Implementation: Implemented in Python.
• Sequence alignment: Requires a local installation of BLAST for sequence alignment tasks.
• Optional QIIME integration: Supports optional integration with QIIME tools for enhanced data processing.

Scientific Applications:

• Epigenetic regulation studies: Allows detailed analysis of methylation patterns involved in gene regulation.
• Cancer genomics: Enables investigation of methylation heterogeneity and epihaplotype variation in cancer samples.
• Developmental biology: Facilitates study of dynamic methylation changes during development at single-molecule resolution.
• Other methylation-focused research: Supports investigations where CpG methylation patterns affect gene expression and cellular function.

Methodology:

Processes targeted deep bisulfite sequencing amplicon reads to perform quantitative and epihaplotype analyses of CpG methylation, uses BLAST for sequence alignment, and optionally integrates QIIME tools.