[Re] Computational Replication of SADDLE: Empirical Next-Generation Sequencing Read Partitions and Primer Interaction Distribution in a 384-Plex PCR Panel

[Re] Computational Replication of SADDLE: Empirical Next-Generation Sequencing Read Partitions and Primer Interaction Distribution in a 384-Plex PCR Panel Author: Rashid Kadayil (ORCID: 0009-0009-6398-4557) Target Journal: ReScience C (ISSN 2430-3658, rescience.github.io) Replication Category: Qualified Partial Replication Public GitHub Code Repository: https://github.com/Rashidmstar12/saddle-replication This reproducibility deposit provides the open-source replication package, derived datasets, and automated verification scripts for an independent computational replication of SADDLE (Xie et al., Nature Communications 13, 1881, 2022; DOI: 10.1038/s41467-022-29500-4; PMID: 35410464). The package confirms the published read classification proportions (~43% on-target, ~56% nonspecific, ~1% primer-dimers) across the 384-plex NGS validation dataset (Sample E19, 3,942,385 reads) within 0.86% absolute difference under our pipeline's derived post-filter classified denominator (N = 2,860,664), corroborates the extreme heavy-tailed concentration of primer-dimers (67.57% in a single dominant pair rp213 x rp371), and provides supplementary exploratory benchmarks evaluating SADDLE Badness heuristics against nearest-neighbor thermodynamics and supervised models.