作用：从测序深度估计 Gifu 与 MG20 的 45S 与 5S rDNA 拷贝数；把 T2T 装配的 rDNA 阵列屏蔽后追加一个 45S 与一个 5S 代表重复构成折叠参考，WGS/HiFi reads 比对后用 mosdepth 量深度，组件深度除以单拷贝 BUSCO 位点深度中位数即得拷贝数，并与装配来源计数并列。
入口：run_rDNA_CN.sh
输入：装配 {PROJ_04_LOTUS_GENOME}/00_assembly_result/{GifuT2T/Lotus_GifuT2T_v1.0.fasta,MG20T2T/Lotus_MG20T2T_v1.0.fasta}；WGS 01_data/<acc>/WGS/<acc>_Clean_R1.fq 与 _R2.fq；HiFi 01_data/<acc>/hifi/<acc>_hifi.fastq.gz；BUSCO 02_assembly/<acc>/08.quality/02.busco/<acc>_lotus/run_embryophyta_odb10/full_table.tsv；rDNA 阵列 BED 03_annotation/<acc>/rDNA/rRNA.bed。
输出：${OUTDIR} = {PROJ_04_LOTUS_GENOME}/03_annotation/rDNA_CN，每材料一个子目录：02_rdna/（rDNA_arrays.bed、代表重复 .fa/.gff）、03_busco/（*_BUSCO_singlecopy.bed）、04_ref/（*_CN_reference.fa 及索引）、05_map/（*_{WGS,HiFi}_CN.bam）、06_depth/（mosdepth *.regions.bed.gz）、07_cn/（*_{WGS,HiFi}_CN_summary.tsv），另有合并表 final_rDNA_CN.tsv。
运行：bash run_rDNA_CN.sh（#CSUB -J rDNA_CN、队列 c01、-n 64、span[hosts=1]；一次提交内先 Gifu 后 MG20）。
工具：bwa mem -t 50；minimap2 -ax map-hifi -t 50；samtools faidx、sort -@ 16、index、flagstat；bedtools maskfasta、intersect -v；mosdepth -t 8 --by <bed>；Barrnap --kingdom euk 校验代表重复；Python 3（pandas、numpy）。
English
**Purpose**: Estimate the 45S and 5S rDNA copy number of Gifu and MG20 from read depth; the rDNA arrays of the T2T assembly are masked and one representative 45S and one representative 5S repeat are appended to form a collapsed reference, WGS and HiFi reads are mapped and depth is measured with mosdepth, and each rDNA component's depth divided by the median depth over single-copy BUSCO loci gives the copy number, set beside the assembly-derived counts.
**Entry point**: `run_rDNA_CN.sh`
**Inputs**: the assemblies `{PROJ_04_LOTUS_GENOME}/00_assembly_result/{GifuT2T/Lotus_GifuT2T_v1.0.fasta,MG20T2T/Lotus_MG20T2T_v1.0.fasta}`; WGS `01_data//WGS/_Clean_R1.fq` and `_R2.fq`; HiFi `01_data//hifi/_hifi.fastq.gz`; BUSCO `02_assembly//08.quality/02.busco/_lotus/run_embryophyta_odb10/full_table.tsv`; the rDNA array BED `03_annotation//rDNA/rRNA.bed`.
**Outputs**: `${OUTDIR}` = `{PROJ_04_LOTUS_GENOME}/03_annotation/rDNA_CN`, one subdirectory per accession: `02_rdna/` (`rDNA_arrays.bed`, the representative repeats `.fa`/`.gff`), `03_busco/` (`*_BUSCO_singlecopy.bed`), `04_ref/` (`*_CN_reference.fa` and indexes), `05_map/` (`*_{WGS,HiFi}_CN.bam`), `06_depth/` (mosdepth `*.regions.bed.gz`), `07_cn/` (`*_{WGS,HiFi}_CN_summary.tsv`), plus the merged table `final_rDNA_CN.tsv`.
**Run**: `bash run_rDNA_CN.sh` (`#CSUB -J rDNA_CN`, queue c01, `-n 64`, `span[hosts=1]`; Gifu then MG20 in one submission).
**Tools**: bwa `mem -t 50`; minimap2 `-ax map-hifi -t 50`; samtools `faidx`, `sort -@ 16`, `index`, `flagstat`; bedtools `maskfasta`, `intersect -v`; mosdepth `-t 8 --by `; Barrnap `--kingdom euk` to verify the representative repeats; Python 3 (pandas, numpy).