BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and...

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• Bulk and single-cell whole-genome DNA methylation data are often under-utilized due to inefficient read mapping and discarded genetic information.
• Existing methods neglect the linkage between epigenetic modifications and genetic variants at the read level.
• Processing single-cell DNA methylation data presents unique challenges in scalability and mappability.

Purpose of the Study:

• To introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its R/Bioconductor package, biscuiteer.
• To enable simultaneous extraction of genetic and epigenetic information from DNA methylation sequencing data.
• To facilitate the analysis of cellular and tissue heterogeneity using coupled epigenetic and genetic information.

Main Methods:

• Development of the BISCUIT toolkit for processing DNA methylation sequencing reads.
• Implementation of the biscuiteer R/Bioconductor package for data analysis.
• Introduction of the epiBED format for single-molecule analysis of linked genetic and epigenetic data.

Main Results:

• BISCUIT enhances read mappability, crucial for single-cell DNA methylation studies.
• The toolkit offers flexibility and scalability for processing large, complex experimental designs.
• Simultaneous extraction of genetic and epigenetic information is achieved, improving data utility.
• The epiBED format supports single-molecule analysis of coupled epigenetic and genetic information.

Conclusions:

• BISCUIT and biscuiteer provide efficient solutions for under-utilized DNA methylation sequencing data.
• These tools are particularly beneficial for single-cell studies, addressing key challenges in data processing.
• The developed methods facilitate a deeper understanding of cellular and tissue heterogeneity through integrated genetic and epigenetic analysis.