biostudies-literatureLiu DPTEN ResearchNICHD NIH HHSCleveland ClinicCleveland Clinic FoundationAmerican Academy of Neurology103357https://www.ebi.ac.uk/biostudies/studies/S-EPMC11489062biostudies-literatureUnknown5(4)Circulating cell-free DNA (cfDNA) fragment end motif profiles are a promising biomarker in precision oncology. Here, we present a protocol for analyzing plasma cfDNA fragment end motifs from ultra-low-pass whole-genome sequencing (WGS) data. We detail a pipeline composed of sequential bash scripts for processing post-alignment BAM files. Subsequently, we outline the procedure for downstream analysis and visualization of 4-mer as well as other n-mer cfDNA end motifs in R. For complete details on the use and execution of this protocol, please refer to Liu et al.¹.STAR protocolsProtocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.PMC11489062R01 HD105049Dhawan ANi YLiu DYehia LEng CfalseProtocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.Circulating cell-free DNA (cfDNA) fragment end motif profiles are a promising biomarker in precision oncology. Here, we present a protocol for analyzing plasma cfDNA fragment end motifs from ultra-low-pass whole-genome sequencing (WGS) data. We detail a pipeline composed of sequential bash scripts for processing post-alignment BAM files. Subsequently, we outline the procedure for downstream analysis and visualization of 4-mer as well as other n-mer cfDNA end motifs in R. For complete details on the use and execution of this protocol, please refer to Liu et al.¹.2024-01-01T00:00:00Z2024 Dec2026-07-01T03:16:36.631Z2025-04-21T21:46:27.891ZS-EPMC114890623936809310.1016/j.xpro.2024.103357