BISCUIT

BISCUIT performs simultaneous inference of DNA methylation and genetic variation from whole-genome bisulfite sequencing data, improving read mappability and enabling single-molecule analysis in bulk and single-cell studies.

Key Features:

• Efficient Mapping: Enhances mappability of bisulfite sequencing reads to improve alignment in bulk and single-cell datasets.
• Comprehensive Data Utilization: Retains and utilizes genetic information alongside epigenetic (DNA methylation) data extracted from bisulfite sequencing.
• Standards-Compliant Output: Generates outputs that adhere to established file standards for compatibility with other bioinformatics tools and workflows.
• Scalability and Flexibility: Processes large-scale experimental designs suitable for bulk and single-cell whole-genome methylation studies.
• EpiBED Format: Produces an epiBED format that encodes single-molecule coupled epigenetic and genetic information for analysis of cellular and tissue heterogeneity.
• biscuiteer (R/Bioconductor): Provides a companion R/Bioconductor package, biscuiteer, for downstream analysis of BISCUIT outputs.

Scientific Applications:

• Single-cell DNA methylation analysis: Processes single-cell whole-genome bisulfite sequencing data to improve read alignment and joint genetic/epigenetic inference.
• Characterization of cellular heterogeneity: Enables investigation of cell-to-cell variation by coupling single-molecule methylation patterns with genetic variation.
• Epigenetic studies of gene regulation: Facilitates comprehensive analyses of DNA methylation patterns across genomes to study regulatory mechanisms.
• Clinical research and diagnostics: Supports large-scale and time-sensitive analyses of methylation data applicable to clinical research contexts.

Methodology:

Enhances mappability of bisulfite sequencing reads, simultaneously extracts genetic and epigenetic information from sequencing data, outputs standards-compliant files including the epiBED single-molecule format, and provides the biscuiteer R/Bioconductor package for downstream analysis.