├── 01_assembly ├── HU-3095.ini ├── Hi-C.sh ├── Hifiasm.sh ├── Hifiasm_trio.sh ├── README.md ├── Survey.sh └── Telomere_local_assembly.sh ├── 02_Polish ├── bin │ ├── README.md │ ├── bin │ │ ├── bam2fbed.py │ │ ├── bam_filter.py │ │ ├── bam_region_depth.py │ │ ├── fxTools │ │ ├── map_one_by_one.py │ │ ├── minimap2 │ │ ├── nextPolish2 │ │ ├── nextpolish1.py │ │ ├── nextpolish1.so │ │ ├── nextpolish2.py │ │ ├── nextpolish2.so │ │ ├── paflift.py │ │ ├── process_bam.py │ │ ├── samtools │ │ └── yak │ ├── lib │ │ ├── __pycache__ │ │ │ ├── kit.cpython-36.pyc │ │ │ └── kit.cpython-37.pyc │ │ └── kit.py │ └── nextp2w.py ├── lib │ ├── 01_yak │ │ ├── tasks │ │ │ └── yak.wdl │ │ └── wf_yak.wdl │ ├── 02_region │ │ ├── tasks │ │ │ └── region.wdl │ │ └── wf_region.wdl │ ├── 03_map_gap │ │ ├── tasks │ │ │ └── map_gap.wdl │ │ └── wf_map_gap.wdl │ ├── 04_nextpolish1 │ │ ├── tasks │ │ │ └── task.wdl │ │ └── wf_nextpolish1.wdl │ ├── 05_nextpolish2_fit │ │ └── tasks │ │ │ └── nextpolish2_fit.wdl │ ├── 06_nextpolish2_nofit │ │ └── tasks │ │ │ └── nextpolish2_nofit.wdl │ ├── 07_merge │ │ └── tasks │ │ │ └── mergefasta.wdl │ └── 08_merge_polish │ │ └── tasks │ │ └── finallypolish.wdl ├── main.wdl ├── run.json ├── run.sh └── software.json ├── 03_Assessment ├── BUSCO.sh ├── Colinearity.sh ├── HiFi.assessment.sh ├── NGS.assessment.sh ├── ONT.assessment.sh ├── QV_assessment.sh └── README.md ├── 04_SD ├── README.md ├── SD.sh ├── circos.conf └── circos.sh ├── 05_Methylation ├── HiFi_cpg_methylation.sh ├── ONT.methylation.sh └── README.md ├── 06_Chip-seq ├── ChIP-seq.sh ├── README.md └── hy.final.peak.bed ├── 07_Annotation ├── Denovo-prediction │ ├── Augustus.hint.sh │ └── Augustus.sh ├── Homolog-based │ └── GeMoma.sh ├── README.md ├── Repeat.anno.sh └── Transcript │ ├── Iso-seq │ ├── Iso-seq.sh │ └── PASA.sh │ └── RNA-seq │ ├── Quality-control.sh │ ├── STAR.sh │ └── Stringtie.sh ├── 08_Centromeres ├── Identity_heatmap.sh ├── NeSSie.sh ├── README.md ├── SDT_pdf_ForNessie.py ├── SRF.sh └── config.yaml ├── 09_OrthoFinder ├── OrthoFinder.sh └── README.md ├── LICENSE └── README.md /01_assembly/HU-3095.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/HU-3095.ini -------------------------------------------------------------------------------- /01_assembly/Hi-C.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/Hi-C.sh -------------------------------------------------------------------------------- /01_assembly/Hifiasm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/Hifiasm.sh -------------------------------------------------------------------------------- /01_assembly/Hifiasm_trio.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/Hifiasm_trio.sh -------------------------------------------------------------------------------- /01_assembly/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/README.md -------------------------------------------------------------------------------- /01_assembly/Survey.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/Survey.sh -------------------------------------------------------------------------------- /01_assembly/Telomere_local_assembly.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/01_assembly/Telomere_local_assembly.sh -------------------------------------------------------------------------------- /02_Polish/bin/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/README.md -------------------------------------------------------------------------------- /02_Polish/bin/bin/bam2fbed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/bam2fbed.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/bam_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/bam_filter.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/bam_region_depth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/bam_region_depth.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/fxTools: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/fxTools -------------------------------------------------------------------------------- /02_Polish/bin/bin/map_one_by_one.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/map_one_by_one.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/minimap2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/minimap2 -------------------------------------------------------------------------------- /02_Polish/bin/bin/nextPolish2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/nextPolish2 -------------------------------------------------------------------------------- /02_Polish/bin/bin/nextpolish1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/nextpolish1.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/nextpolish1.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/nextpolish1.so -------------------------------------------------------------------------------- /02_Polish/bin/bin/nextpolish2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/nextpolish2.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/nextpolish2.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/nextpolish2.so -------------------------------------------------------------------------------- /02_Polish/bin/bin/paflift.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/paflift.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/process_bam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/process_bam.py -------------------------------------------------------------------------------- /02_Polish/bin/bin/samtools: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/samtools -------------------------------------------------------------------------------- /02_Polish/bin/bin/yak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/bin/yak -------------------------------------------------------------------------------- /02_Polish/bin/lib/__pycache__/kit.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/lib/__pycache__/kit.cpython-36.pyc -------------------------------------------------------------------------------- /02_Polish/bin/lib/__pycache__/kit.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/lib/__pycache__/kit.cpython-37.pyc -------------------------------------------------------------------------------- /02_Polish/bin/lib/kit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/lib/kit.py -------------------------------------------------------------------------------- /02_Polish/bin/nextp2w.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/bin/nextp2w.py -------------------------------------------------------------------------------- /02_Polish/lib/01_yak/tasks/yak.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/01_yak/tasks/yak.wdl -------------------------------------------------------------------------------- /02_Polish/lib/01_yak/wf_yak.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/01_yak/wf_yak.wdl -------------------------------------------------------------------------------- /02_Polish/lib/02_region/tasks/region.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/02_region/tasks/region.wdl -------------------------------------------------------------------------------- /02_Polish/lib/02_region/wf_region.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/02_region/wf_region.wdl -------------------------------------------------------------------------------- /02_Polish/lib/03_map_gap/tasks/map_gap.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/03_map_gap/tasks/map_gap.wdl -------------------------------------------------------------------------------- /02_Polish/lib/03_map_gap/wf_map_gap.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/03_map_gap/wf_map_gap.wdl -------------------------------------------------------------------------------- /02_Polish/lib/04_nextpolish1/tasks/task.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/04_nextpolish1/tasks/task.wdl -------------------------------------------------------------------------------- /02_Polish/lib/04_nextpolish1/wf_nextpolish1.wdl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /02_Polish/lib/05_nextpolish2_fit/tasks/nextpolish2_fit.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/05_nextpolish2_fit/tasks/nextpolish2_fit.wdl -------------------------------------------------------------------------------- /02_Polish/lib/06_nextpolish2_nofit/tasks/nextpolish2_nofit.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/06_nextpolish2_nofit/tasks/nextpolish2_nofit.wdl -------------------------------------------------------------------------------- /02_Polish/lib/07_merge/tasks/mergefasta.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/07_merge/tasks/mergefasta.wdl -------------------------------------------------------------------------------- /02_Polish/lib/08_merge_polish/tasks/finallypolish.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/lib/08_merge_polish/tasks/finallypolish.wdl -------------------------------------------------------------------------------- /02_Polish/main.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/main.wdl -------------------------------------------------------------------------------- /02_Polish/run.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/run.json -------------------------------------------------------------------------------- /02_Polish/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/run.sh -------------------------------------------------------------------------------- /02_Polish/software.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/02_Polish/software.json -------------------------------------------------------------------------------- /03_Assessment/BUSCO.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/BUSCO.sh -------------------------------------------------------------------------------- /03_Assessment/Colinearity.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/Colinearity.sh -------------------------------------------------------------------------------- /03_Assessment/HiFi.assessment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/HiFi.assessment.sh -------------------------------------------------------------------------------- /03_Assessment/NGS.assessment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/NGS.assessment.sh -------------------------------------------------------------------------------- /03_Assessment/ONT.assessment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/ONT.assessment.sh -------------------------------------------------------------------------------- /03_Assessment/QV_assessment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/QV_assessment.sh -------------------------------------------------------------------------------- /03_Assessment/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/03_Assessment/README.md -------------------------------------------------------------------------------- /04_SD/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/04_SD/README.md -------------------------------------------------------------------------------- /04_SD/SD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/04_SD/SD.sh -------------------------------------------------------------------------------- /04_SD/circos.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/04_SD/circos.conf -------------------------------------------------------------------------------- /04_SD/circos.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/04_SD/circos.sh -------------------------------------------------------------------------------- /05_Methylation/HiFi_cpg_methylation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/05_Methylation/HiFi_cpg_methylation.sh -------------------------------------------------------------------------------- /05_Methylation/ONT.methylation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/05_Methylation/ONT.methylation.sh -------------------------------------------------------------------------------- /05_Methylation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/05_Methylation/README.md -------------------------------------------------------------------------------- /06_Chip-seq/ChIP-seq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/06_Chip-seq/ChIP-seq.sh -------------------------------------------------------------------------------- /06_Chip-seq/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/06_Chip-seq/README.md -------------------------------------------------------------------------------- /06_Chip-seq/hy.final.peak.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/06_Chip-seq/hy.final.peak.bed -------------------------------------------------------------------------------- /07_Annotation/Denovo-prediction/Augustus.hint.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Denovo-prediction/Augustus.hint.sh -------------------------------------------------------------------------------- /07_Annotation/Denovo-prediction/Augustus.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Denovo-prediction/Augustus.sh -------------------------------------------------------------------------------- /07_Annotation/Homolog-based/GeMoma.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Homolog-based/GeMoma.sh -------------------------------------------------------------------------------- /07_Annotation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/README.md -------------------------------------------------------------------------------- /07_Annotation/Repeat.anno.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Repeat.anno.sh -------------------------------------------------------------------------------- /07_Annotation/Transcript/Iso-seq/Iso-seq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Transcript/Iso-seq/Iso-seq.sh -------------------------------------------------------------------------------- /07_Annotation/Transcript/Iso-seq/PASA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Transcript/Iso-seq/PASA.sh -------------------------------------------------------------------------------- /07_Annotation/Transcript/RNA-seq/Quality-control.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Transcript/RNA-seq/Quality-control.sh -------------------------------------------------------------------------------- /07_Annotation/Transcript/RNA-seq/STAR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Transcript/RNA-seq/STAR.sh -------------------------------------------------------------------------------- /07_Annotation/Transcript/RNA-seq/Stringtie.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/07_Annotation/Transcript/RNA-seq/Stringtie.sh -------------------------------------------------------------------------------- /08_Centromeres/Identity_heatmap.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/08_Centromeres/Identity_heatmap.sh -------------------------------------------------------------------------------- /08_Centromeres/NeSSie.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/08_Centromeres/NeSSie.sh -------------------------------------------------------------------------------- /08_Centromeres/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/08_Centromeres/README.md -------------------------------------------------------------------------------- /08_Centromeres/SDT_pdf_ForNessie.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/08_Centromeres/SDT_pdf_ForNessie.py -------------------------------------------------------------------------------- /08_Centromeres/SRF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/08_Centromeres/SRF.sh -------------------------------------------------------------------------------- /08_Centromeres/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/08_Centromeres/config.yaml -------------------------------------------------------------------------------- /09_OrthoFinder/OrthoFinder.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/09_OrthoFinder/OrthoFinder.sh -------------------------------------------------------------------------------- /09_OrthoFinder/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/09_OrthoFinder/README.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lly1214/CAU-T2T-Sheep/HEAD/README.md --------------------------------------------------------------------------------