CODEC Library Preparation From Genomic DNA

Concatenating Original Duplex for Error Correction (CODEC) is a duplex sequencing library preparation method that physically links the Watson and Crick strands of individual DNA molecules. Despite growing interest in cost-effective duplex sequencing such as CODEC, broader adoption can be limited by the lack of detailed, step-by-step wet-lab workflows. Here, we describe an experimentally validated protocol for preparing CODEC libraries from genomic DNA that are compatible with standard Illumina platforms. The protocol incorporates blunt-end fragmentation, dideoxy base-blocked A-tailing, CODEC adapter ligation, strand-displacing extension, and library amplification, with quality-control checkpoints, critical parameters, and troubleshooting guidance. In addition, we provide an optional matched germline reference library preparation protocol to support somatic variant calling. This workflow is intended to facilitate reproducible implementation of CODEC in molecular biology laboratories for research applications requiring accurate detection of low-frequency somatic variants. © 2026 Wiley Periodicals LLC. Support Protocol 1: CODEC oligonucleotide ordering and synthesis Support Protocol 2: CODEC quadruplex adapter synthesis Basic Protocol 1: CODEC library preparation from genomic DNA Support Protocol 3: AMPure XP/SPRIselect bead cleanup Basic Protocol 2: Matched germline reference library preparation from genomic DNA.