├── .DS_Store ├── .gitignore ├── LICENSE ├── README.md ├── cosigt.go ├── cosigt.mod.png └── cosigt_smk ├── README.md └── workflow ├── Snakefile ├── envs ├── bedtools.yaml ├── bwa-mem2.yaml ├── cosigt.yaml ├── gafpack.yaml ├── gfainject.yaml ├── impg.yaml ├── kfilt.yaml ├── minimap2.yaml ├── odgi.yaml ├── pangene.yaml ├── panplexity.yaml ├── pggb.yaml ├── python.yaml ├── r.yaml ├── samtools.yaml └── wally.yaml ├── rules ├── bedtools.smk ├── benchmark.smk ├── bwa-mem2.smk ├── cosigt.smk ├── gafpack.smk ├── gfainject.smk ├── impg.smk ├── kfilt.smk ├── minimap2.smk ├── odgi.smk ├── pangene.smk ├── pggb.smk ├── refine.smk └── samtools.smk └── scripts ├── app.r ├── bedpe_filter.sh ├── bedpe_filter_refine.sh ├── bedpe_merge.sh ├── calc_tpr.r ├── calculate_qv.sh ├── cluster.r ├── combine_tpr_qv.r ├── compute_qv.cpp ├── convert_bed.sh ├── coverage_outliers.r ├── filter.r ├── make_mask_files.sh ├── make_minimap2_batches.sh ├── organize.py ├── pangene_prepare.sh ├── plot_tpr.r ├── plotava.r ├── plotgggenes.r ├── prepare_qv.sh ├── runapp.sh └── viz_odgi.r /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/.DS_Store -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/README.md -------------------------------------------------------------------------------- /cosigt.go: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt.go -------------------------------------------------------------------------------- /cosigt.mod.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt.mod.png -------------------------------------------------------------------------------- /cosigt_smk/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/README.md -------------------------------------------------------------------------------- /cosigt_smk/workflow/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/Snakefile -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/bedtools.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/bedtools.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/bwa-mem2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/bwa-mem2.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/cosigt.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/cosigt.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/gafpack.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/gafpack.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/gfainject.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/gfainject.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/impg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/impg.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/kfilt.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/minimap2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/minimap2.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/odgi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/odgi.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/pangene.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/panplexity.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/panplexity.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/pggb.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/pggb.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/python.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/python.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/r.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/r.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/samtools.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/samtools.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/envs/wally.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/envs/wally.yaml -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/bedtools.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/bedtools.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/benchmark.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/benchmark.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/bwa-mem2.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/bwa-mem2.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/cosigt.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/cosigt.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/gafpack.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/gafpack.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/gfainject.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/gfainject.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/impg.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/impg.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/kfilt.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/kfilt.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/minimap2.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/minimap2.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/odgi.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/odgi.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/pangene.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/pangene.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/pggb.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/pggb.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/refine.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/refine.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/rules/samtools.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/rules/samtools.smk -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/app.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/app.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/bedpe_filter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/bedpe_filter.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/bedpe_filter_refine.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/bedpe_filter_refine.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/bedpe_merge.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/bedpe_merge.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/calc_tpr.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/calc_tpr.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/calculate_qv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/calculate_qv.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/cluster.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/cluster.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/combine_tpr_qv.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/combine_tpr_qv.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/compute_qv.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/compute_qv.cpp -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/convert_bed.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/convert_bed.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/coverage_outliers.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/coverage_outliers.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/filter.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/filter.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/make_mask_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/make_mask_files.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/make_minimap2_batches.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/make_minimap2_batches.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/organize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/organize.py -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/pangene_prepare.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/pangene_prepare.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/plot_tpr.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/plot_tpr.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/plotava.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/plotava.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/plotgggenes.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/plotgggenes.r -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/prepare_qv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/prepare_qv.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/runapp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/runapp.sh -------------------------------------------------------------------------------- /cosigt_smk/workflow/scripts/viz_odgi.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/davidebolo1993/cosigt/HEAD/cosigt_smk/workflow/scripts/viz_odgi.r --------------------------------------------------------------------------------