2026-10-12T15:00:27Z https://www.scidb.cn/oai

10.57760/sciencedb.j00210.00035 2025-09-11T07:48:30Z

2025-09-11 305-high-quality-SV-dataset-of-3KRGP doi:10.57760/sciencedb.j00210.00035 en The R pipelines (BWGS) and bash workflows for rice genomic analysis. Three marker strategies are supported:variant_calling: Stand‑alone bash scripts for variant discovery (SNP/INDEL with GATK; SV with Delly)SNP: SNP‑only GS workflowsSV: SV‑only GS workflows (raw / genic / intergenic)Both: Combined SNP + SV GS workflowsEach sub‑folder contains:One or more core R scripts (BWGS_with_*.R) that run 5‑fold × 10‑repeat cross‑validation on up to ten GS models (GBLUP, RF, EGBLUP, RR, BRR, LASSO, EN, BL, BB, RKHS).Shell wrappers (run_*.sh) that set the working directory and call the corresponding R script for a specific GWAS filtering threshold (p < 0.05 / 0.01 / 0.001 or “whole” set).The scripts and pipelines for the study are also accessible in https://github.com/lianglunping/305-high-quality-SV-dataset-of-3KRGP/tree/main. rice; genomic analysis; SV dataset Lunping Liang Chaopu Zhang Linjun Yu Tingting Sheng Shuyue Zheng Shijiao Li Shuran Zhou Ting Feng Fan Zhang Zhikang Li Yanru Cui Wensheng Wang Min Li PUBLIC https://api.github.com/licenses/gpl-3.0 dataset http://www.doi.org/10.1016/j.cj.2025.08.005 Science Data Bank