For combined methylation and fragmentomics, SRSLY enables preservation of native fragment ends by performing adapter ligation before methyl conversion (“downstream conversion”). This workflow retains native termini while enabling methylation analysis. In these applications, gentler conversion chemistries—such as NEBNext EM-seq V2 or TAPS+—are recommended to minimize damage to the ligated library and maximize template fidelity.

For standard methylation profiling, both enzymatic and bisulfite conversion methods are compatible. Even when conversion further shortens cfDNA fragments, the SRSLY library efficiently captures these smaller molecules. If targeted enrichment follows, however, hybrid capture workflows and probe design should be optimized to accommodate the shorter fragment distribution.

Methylation profiling — with or without targeted enrichment — is the predominant application of Methyl-Seq. Bisulfite conversion remains a common choice for methyl-conversion chemistry, and SRSLY's ForShear enzymatic fragmentation module generates sequencer-compatible fragment sizes downstream of conversion, with minimal DNA loss despite conversion-induced degradation. From there, a standard hybrid-capture protocol can be layered on to enrich for the regions or variants of interest.