A Reproducible Pipeline for Human Reference Genome (hg38) Setup and Gene Feature Extraction: PRNP and NEFL Case Studies

This white paper presents a reproducible, workstation-scale pipeline for setting up the human reference genome (hg38) with GENCODE v46 annotations and deriving gene-specific assets for PRNP (prion protein) and NEFL (neurofilament light). The methodology is optimized for macOS environments using a Homebrew-managed bioinformatics toolchain and is suitable for rapid on-the-job training (OJT), independent research, and publication-ready reproducibility. The workflow covers: Acquisition and indexing of the hg38 reference genome. Integration of GENCODE v46 basic annotations. Generation of transcriptome and coding sequence FASTA datasets. Locus-specific extraction of PRNP and NEFL transcripts, coding sequences, and promoter windows. Preliminary motif reconnaissance within ±1 kb of transcription start sites. This pipeline is validated against expected gene models and promoter motifs, with attention to reproducibility, governance, and troubleshooting. It provides a foundation for downstream neuro-oncology and rare-disease research applications, including biomarker discovery, transcription factor binding site analysis, and variant annotation overlays. Keywords: hg38, GENCODE, reference genome, gene feature extraction, PRNP, NEFL, prion protein, neurofilament light, promoter analysis, motif discovery, reproducible pipeline, bioinformatics