Avifaunal-scale genomic erosion in a biodiversity hotspot sounds a conservation alarm

This dataset contains all custom scripts and computational workflows used for data processing, genomic analysis, and statistical modeling in this study.  Genome assembly: Scripts for read processing (BBMap), k‑mer estimation (KmerGenie), assembly (Abyss), synteny-based anchoring (Satsuma), and completeness assessment (BUSCO).Resequencing and alignment: Workflows for DNA damage correction (mapDamage), mapping (BWA-MEM), sorting and deduplication (Sambamba, GATK), and genotype likelihood estimation (ANGSD).  Population genomics: Scripts for demographic reconstruction (SMC++), neutral region definition (GERP scores, LiftOver), and diversity estimation (Watterson's θ, heterozygosity, Tajima's D, FST).  Statistical analyses: R scripts implementing Bayesian models (MCMCglmm), Random Forest regression (randomForest), and generalized additive models (mgcv).  All code is organized by analytical steps in the article with detailed comments.