QUMA

QUMA analyzes bisulfite sequencing data to align reads and quantify DNA methylation at CpG sites for epigenetic and disease-association studies.

Key Features:

• Comprehensive data processing: Integrates sequence alignment and methylation quantification specifically for bisulfite sequencing data.
• Accepted input types: Processes PCR target genomic sequences and raw bisulfite sequences for downstream analysis.
• Alignment visualization: Visualizes sequence alignments to assess methylation patterns at individual CpG sites.
• Quality control parameters: Provides adjustable cutoff settings for aligned sequence quality to control inclusion of reads in analysis.

Scientific Applications:

• DNA methylation profiling: Generates quantitative methylation profiles from bisulfite sequencing data for locus-specific analysis.
• Epigenetic and disease-association studies: Supports investigations of gene regulation and disease correlations via CpG methylation measurements.

Methodology:

Aligns bisulfite-treated sequences against a reference genome, visualizes alignments, and quantifies methylation levels at CpG sites, with adjustable cutoffs for alignment quality and support for processing PCR target and raw bisulfite sequences for high-throughput datasets.