ValleScope paper reproducibility package

This record provides a publication snapshot of the processed data, scripts, command logs, and figure outputs used for the ValleScope manuscript, entitled “ValleScope: context-based correspondence assignment for satellite DNA in telomere-to-telomere assemblies”. The directory structure is organized by manuscript figures (fig2–fig6) and supplementary figures (supp_fig2–supp_fig8). Each directory contains processed files, scripts, command logs, and/or figure panels used to generate the corresponding results. This package is intended to support transparency and reproducibility of the published analyses. It is not a complete raw-data reprocessing workflow. Large public genome assemblies and external annotations should be obtained from their original sources, as described in the manuscript and Supplementary Materials. Installation scripts for the HPRC and HGSVC assemblies used in this study are provided in the data_install/HPRC and data_install/HGSVC directories, respectively. Summary tables for the data used to generate the manuscript figures are provided in 2026_NAR_data_for_fig.xlsx and 2026_NAR_data_for_fig_2.xlsx. ValleScope itself is available at: https://github.com/hiura-censat/ValleScope