A framework for peptide identification on commercial nanopore sequencing platforms

This Zenodo repository contains datasets and processed results associated with “A framework for peptide identification on commercial nanopore sequencing platforms” (Beslic et al., 2026). It includes a subset of raw nanopore POD5 data (data_pod5_2variants_reduced.tar.gz), basecalling results, alignment and segmentation results for the subset (results_basecalls_alignments_2variants.tar.gz), segmentation results for the full dataset (results_PLRs_only.tar.gz), and condensed classification outputs required for figure and metric reproduction (results_classification_only.tar.gz). The analysis workflow and code are provided in code.tar.gz and correspond to https://github.com/ZKI-PH-ImageAnalysis/nanopore-peptide-identification (v0.1.0). The POD5 dataset contains selected βCAT measurements (two variants and one βCAT-WW run) and is sufficient to understand and reproduce the segmentation and preprocessing pipeline, but not the full dataset used in the study. The complete raw POD5 dataset (>500 GB) is not included due to storage limitations. Additional intermediate data can be provided upon reasonable request. Due to variability in Dorado basecalling across hardware and software configurations, minor differences may occur when re-running the pipeline from raw data. Precomputed intermediate outputs are provided to ensure exact reproducibility of figures and reported metrics.