biostudies-literatureUnknownZhang ZNCI NIH HHSEpigenomic profiling of circulating chromatin is a powerful and minimally invasive approach for detecting and monitoring disease, but there are no bioinformatics pipelines tailored to the unique characteristics of cell-free chromatin. We present SNAP (Streamlined Nextflow Analysis Pipeline), a reproducible, scalable, and modular workflow specifically designed for immunoprecipitation-based methods for profiling cell-free chromatin. SNAP incorporates quality control metrics optimized for circulating chromatin, including enrichment score and fragment count thresholds, as well as direct estimation of circulating tumor DNA (ctDNA) content from fragment length distributions. It also includes SNP fingerprinting to enable sample identity verification. When applied to cfChIP-seq and cfMeDIP-seq datbioRxiv : the preprint server for biology2025.12.30.694452https://www.ebi.ac.uk/biostudies/studies/S-EPMC12776326biostudies-literatureSNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.PMC12776326U01 CA296432Canniff JSavignano HSemaan KOsei-Hwedieh DDa Silva Cordeiro PNawfal RBaca SCChhetri SBGulati GWeiss KRBian WHeim TEFortunato BPainter CVasseur DChehade REHSeo JHJin ZPhillips NEid MFreedman MLZhang ZSotudian SHemauer CLee GGfalseSNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.Epigenomic profiling of circulating chromatin is a powerful and minimally invasive approach for detecting and monitoring disease, but there are no bioinformatics pipelines tailored to the unique characteristics of cell-free chromatin. We present SNAP (Streamlined Nextflow Analysis Pipeline), a reproducible, scalable, and modular workflow specifically designed for immunoprecipitation-based methods for profiling cell-free chromatin. SNAP incorporates quality control metrics optimized for circulating chromatin, including enrichment score and fragment count thresholds, as well as direct estimation of circulating tumor DNA (ctDNA) content from fragment length distributions. It also includes SNP fingerprinting to enable sample identity verification. When applied to cfChIP-seq and cfMeDIP-seq dat2025-01-01T00:00:00Z2025 Dec2026-06-04T03:20:29.375Z2026-06-04T03:12:51.259ZS-EPMC127763264150921710.64898/2025.12.30.694452