Medaka genome datasets and codes

```data/├── assembly_v2.3/ # v2.3 assemblies (chromosome-orientation-corrected v2.2.4)│ ├── {Hd-rR,HNI,HSOK}.v2.3.fasta # Scaffolds (chromosomes only)│ └── {Hd-rR,HNI,HSOK}.v2.3.fasta.fai├── assembly_v3.1/ # v3.1 assemblies│ ├── Hd-rR_freeze-20240613/│ │ ├── Hd-rR.freeze-20240613.fasta # Scaffolds│ │ ├── Hd-rR.freeze-20240613.fasta.fai│ │ ├── Hd-rR.freeze-20240613.for_ddbj.fasta # Scaffolds registered to DDBJ (renamed unlocalized)│ │ ├── Hd-rR.freeze-20240613.repeatmasker.bed # RepeatMasker output (root species)│ │ ├── Hd-rR.freeze-20240613.trf.txt # Tandem Repeat Finder output│ │ ├── Hd-rR.freeze-20240613.centromere.bed # Curated centromeric satellite array regions│ │ ├── Hd-rR.freeze-20240613.telomere.bed # Telomere arrays (>100 copies)│ │ ├── Hd-rR.freeze-20240613.teratorn.bed # Teratorn transposon copies (BLAST with TIRs)│ │ ├── Hd-rR.freeze-20240613.tol2.bed # Tol2 (D84375.2) hits│ │ ├── Hd-rR.freeze-20240613.45S.bed # 45S rDNA array regions (>80% full-length)│ │ ├── Hd-rR.freeze-20240613.5S.bed # 5S rDNA array regions (>80% full-length)│ │ ├── Hd-rR.freeze-20240613.dmy.bed # Dmy exon locations (lifted over from v2)│ │ ├── Hd-rR.freeze-20240613.cpg.ont.bed.gz # CpG methylation levels from ONT reads (Modkit)│ │ └── Orylat_protein_240710.{gff3,gtf}.gz{,.tbi} # Gene models (Hd-rR)│ ├── HNI_freeze-20241129/ # Same structure as Hd-rR_freeze-20240613│ │ └── Oryzias_HNI_2025_03_06.gff.gz{,.tbi} # Gene models (HNI)│ └── HSOK_freeze-20241129/ # Same structure as Hd-rR_freeze-20240613│ └── Oryzias_HSOK_2025_03_06.gff.gz{,.tbi} # Gene models (HSOK)├── centromere/│ ├── cen.v3_SF_reprs.fasta # Consensus sequences for SF1–SF5│ ├── cen.v3_chrom_reprs.wo_div_mon.fasta # Per-chromosome representative monomers (excl. divergent/monomeric)│ ├── cen.v3_chrom_reprs.wo_div_mon.mega_phylo.swapped.nwk # Phylogenetic tree (MEGA)│ ├── SF1.cons+repr_units.hyper+hypo.gfa # SF1 monomer graph (hyper/hypo-methylated)│ ├── SF1.repr_units.hyper.fasta # SF1 hyper-methylated representative monomers│ ├── SF1.repr_units.hypo.fasta # SF1 hypo-methylated representative monomers│ ├── SF3.cons+repr_units.hyper+hypo.gfa # SF3 monomer graph (hyper/hypo-methylated)│ ├── SF3.repr_units.hyper.fasta # SF3 hyper-methylated representative monomers│ └── SF3.repr_units.hypo.fasta # SF3 hypo-methylated representative monomers├── rDNA/│ ├── 45S.repr.fasta # 45S rDNA representative unit sequence│ └── 5S.repr.fasta # 5S rDNA representative unit sequence├── sex_dif_region/│ ├── {Hd-rR,HNI}.XSR.bed # X-dif region on Chr X│ ├── {Hd-rR,HNI}.YSR.bed # Y-dif region on Chr Y│ ├── {Hd-rR,HNI}.XSR.vs_{HNI,Hd-rR}.bed # X-dif region coordinates used for comparison│ └── {Hd-rR,HNI}.YSR.vs_{HNI,Hd-rR}.bed # Y-dif region coordinates used for comparison├── syri/│ └── {Hd-rR.HNI,Hd-rR.HSOK,HNI.HSOK,HNI.Hd-rR}.syri.out # SyRI output (whole genome)└── syri_chrXY/ └── {ref_seq}.{query_seq}.syri.out # SyRI output (X/Y-dif regions) code/├── jupyter_notebooks/│ ├── 01-curation 01–20 *.ipynb # Assembly curation code for each strain/version│ ├── 02-centromere 01–05 *.ipynb # Centromere analysis code│ ├── 03-comparative genome analysis.ipynb # Comparative genomics analysis code│ ├── curation.py # Shared scripts for 01-curation* notebooks│ ├── centromere.py # Shared scripts for 02-centromere* notebooks│ └── comparative.py # Shared scripts for 03-comparative* notebook└── scripts/ ├── config.sh # Tool versions (Lmod modules) and pipeline parameters ├── assembly/ │ ├── 01-hifiasm.sh # De novo assembly with Hifiasm │ ├── 01-verkko.sh # De novo assembly with Verkko │ ├── 02-ragtag.sh # Scaffolding with RagTag │ ├── 03-merqury.sh # K-mer QV with Merqury │ ├── 04-winnowmap-hifi.sh # HiFi read mapping with Winnowmap │ ├── 04-winnowmap-ont.sh # ONT read mapping with Winnowmap │ ├── 05-deepvariant-hifi.sh # Variant calling from HiFi mappings with DeepVariant │ ├── 05-deepvariant-ont.sh # Variant calling from ONT mappings with DeepVariant │ ├── 06-modkit.sh # CpG methylation from ONT mappings with Modkit │ ├── 07-mapqv.sh # Mapping-based QV │ ├── 08-repeatmasker.sh # RepeatMasker (root species) │ ├── 09-trf.sh # Tandem repeat detection with TRF │ ├── 10-teratorn.sh # Rough Teratorn annotation by minimap2 mapping │ ├── 11-tol2.sh # Tol2 annotation by minimap2 mapping │ ├── 12-rDNA-45S.sh # 45S rDNA array annotation by minimap2 mapping │ ├── 12-rDNA-5S.sh # 5S rDNA array annotation by minimap2 mapping │ └── 13-cen.sh # Centromere unit decomposition with StringDecomposer ├── comparative/ │ ├── count_sv.py # Count SVs (>=50 bp INS/DEL/INV) from SyRI output │ ├── dmy.sh # Map Dmy (v2) to v3.1 assemblies │ ├── mummer.sh # Whole-genome alignment with MUMmer │ ├── syri.sh # Structural rearrangements with SyRI │ └── syri_chrXY.sh # SyRI for X/Y-dif regions between Hd-rR and HNI ├── curation/ │ ├── map_hic/ │ │ └── run_hic.sh # Map Hi-C reads with Arima Pipeline │ ├── ont_patch/ # ONT-read-based misassembly patching pipeline │ │ ├── run.sh # Main driver │ │ └── scripts/ │ │ ├── find_backbone.py # Find flanking backbone sequences of a misassembly │ │ ├── main.py # Core patching logic using ONT reads │ │ ├── main.sh # Shell wrapper │ │ ├── make_patch.py # Construct patched FASTA │ │ └── eval.sh # Evaluate patch quality by read remapping │ └── verkko_liftover/ # Lift over intervals in Verkko contigs to Hifiasm contigs │ ├── liftover.sh # Run liftover with LiftOff │ ├── process_bed.sh # Initial processing of liftover BED │ └── postprocess_bed.sh # Final filtering and clean-up of liftover BED └── teratorn/ ├── main.sh # Run BLAST and convert output to BED └── blast_output_to_bed_w_queryname.pl # Helper script```