JEEPERS (Jagged-End Error Polishing of Enzymatically misRepaired Sequences) is an innovative computational tool designed to enhance the accuracy of DNA methylation analysis in cell-free DNA (cfDNA) samples. By addressing the challenges posed by jagged ends—single-stranded overhangs on double-stranded DNA fragments—JEEPERS improves the reliability of methylation profiling while preserving the integrity of cfDNA. Operating at the fragment level, the JEEPERS algorithm detects and corrects end-repair-induced errors, enabling precise methylation characterization and simultaneous single nucleotide variant (SNV) genotyping.

Detailed principles and usage instructions for JEEPERS can be found at:

https://code.stanford.edu/alizadeh-diehn/jeepers

The code and data used to generate the figures in the publication by Wang et al. are available for download on the website after registration.