GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE317nnn/GSE317007/primaryOK200OtherHomo sapiensOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE317007GEOGSEfalseFLARE: a Long-Read Nanopore Fragmentomics Pipeline Integrating Copy Number, Methylation, and End-Motif Analysis for Liquid BiopsyCell-free DNA (cfDNA) fragmentation patterns encode biologically and clinically relevant information beyond fragment length, reflecting nuclease activity, chromatin organization, and tissue of origin. Fragmentomics has therefore emerged as a promising strategy to enhance circulating tumor DNA (ctDNA) detection, particularly in cancers with low tumor fractions. However, most existing approaches are optimized for short-read sequencing, limiting their applicability to third-generation platforms. Here, we present FLARE (Fragmentation and Long-read Analysis of Regulatory Epigenetics), an integrated and scalable fragmentomics pipeline specifically optimized for Oxford Nanopore long-read sequencing. FLARE preserves native cfDNA fragment ends and enables the simultaneous analysis of copy number alterations, tumor fraction estimation, methylation-derived signals, fragment length distributions, and 5′ end-motif profiles.2026/04/01GSE317007GSM9463741GSM9463740GSM9463732GSM9463731GSM9463742GSM9463734GSM9463733GSM9463736GSM9463735GSM9463738GSM9463737GSM946373926167317007Homo sapiens[41908150]