Go to figures here https://zenodo.org/uploads/10785693 having the structure:
- Fig_1 - Biorender
- Fig_2
- Fig_3
- Fig_4
- Supplemental_Fig_S1
- Supplemental_Fig_S2
- Supplemental_Fig_S3
- Supplemental_Fig_S4
- Supplemental_Fig_S5
- Supplemental_Fig_S6
- Supplemental_Fig_S7 - Validate_shasta_vs_decoil_vs_cresil.ipynb
- Supplemental_Fig_S8
- Supplemental_Fig_S9
- Supplemental_Fig_S10 - Biorender
- Supplemental_Fig_S11 - Biorender
figures
├── Figure2
│ ├── Validate_shasta_vs_decoil_vs_cresil.ipynb
│ ├── collect_metrics.txt
│ ├── collect_metrics_cresil.txt
│ ├── collect_metrics_decoil_v112.txt
│ ├── collect_metrics_shasta.txt
│ ├── figures
│ │ ├── decoil_shasta_cresil_comparison_alignment.png
│ │ ├── decoil_shasta_cresil_comparison_auN.png
│ │ ├── decoil_shasta_cresil_comparison_auN_all.png
│ │ └── decoil_shasta_cresil_comparison_ident.png
│ ├── sim_263
│ ├── sim_39
│ │ └── reconstruct_v102
│ │ ├── clean.vcf
│ │ ├── reconstruct.bed
│ │ ├── reconstruct.fasta
│ │ ├── reconstruct.json
│ │ ├── reconstruct.links.txt
│ │ ├── reconstruct.pdf
│ │ └── summary.txt
│ ├── sim_6
│ │ └── reconstruct_v102
│ │ ├── clean.vcf
│ │ ├── reconstruct.bed
│ │ ├── reconstruct.fasta
│ │ ├── reconstruct.json
│ │ ├── reconstruct.links.txt
│ │ ├── reconstruct.pdf
│ │ └── summary.txt
│ ├── sim_75
│ │ └── reconstruct_v102
│ │ ├── clean.vcf
│ │ ├── reconstruct.bed
│ │ ├── reconstruct.fasta
│ │ ├── reconstruct.json
│ │ ├── reconstruct.links.txt
│ │ ├── reconstruct.pdf
│ │ └── summary.txt
│ ├── sim_876
│ │ └── reconstruct_v102
│ │ ├── clean.vcf
│ │ ├── reconstruct.bed
│ │ ├── reconstruct.fasta
│ │ ├── reconstruct.json
│ │ ├── reconstruct.links.txt
│ │ ├── reconstruct.pdf
│ │ └── summary.txt
│ ├── sim_946
│ │ └── reconstruct_v102
│ │ ├── clean.vcf
│ │ ├── reconstruct.bed
│ │ ├── reconstruct.fasta
│ │ ├── reconstruct.json
│ │ ├── reconstruct.links.txt
│ │ ├── reconstruct.pdf
│ │ └── summary.txt
│ ├── sim_96
│ │ └── reconstruct_v102
│ │ ├── clean.vcf
│ │ ├── reconstruct.bed
│ │ ├── reconstruct.fasta
│ │ ├── reconstruct.json
│ │ ├── reconstruct.links.txt
│ │ ├── reconstruct.pdf
│ │ └── summary.txt
│ ├── sim_ids.txt
│ ├── summary_merged_v108.txt
│ └── validation_v108.txt
├── Figure3
│ ├── AmpliconRecovery.ipynb
│ ├── CHP212_TR14_dilutions_100perc_single_format.pdf
│ ├── CHP212_TR14_dilutions_10perc_single_format.pdf
│ ├── CHP212_TR14_dilutions_50perc_single_format.pdf
│ └── breakpoints_recovery_merged.pdf
├── Figure4_and_SupplFigS5
│ ├── Figure4_and_SupplFigS5_plots_02112023.ipynb
│ ├── Figure4_patient1.pdf
│ ├── Figure4_patient2.pdf
│ ├── Figure4_patient3.pdf
│ ├── Figure4_patient4.pdf
│ ├── Figure4_patient5.pdf
│ ├── data
│ │ ├── decoil_cellline_calls_ecDNA_decoil_v108_01072023.txt
│ │ ├── decoil_primary_patients_calls_ecDNA_decoil_v110_14102023.txt
│ │ ├── decoil_primary_patients_calls_ecDNA_top3_decoil_v110_14102023.txt
│ │ ├── reconstruct_all_celllines_decoil_v108_01072023.txt
│ │ ├── reconstruct_all_patients_decoil_v110_14102023.txt
│ │ ├── reconstruct_ecDNA_celllines_decoil_v108_01072023.txt
│ │ ├── summary_celllines_decoil_v108_01072023.txt
│ │ ├── summary_celllines_decoil_v108_01072023_filtered.txt
│ │ ├── summary_primary_patients_decoil_v110_14102023.txt
│ │ ├── summary_primary_patients_decoil_v110_14102023_filtered.txt
│ │ └── summary_primary_patients_decoil_v110_14102023_filtered_top3.txt
│ └── figures_v110
│ ├── cn_cumm.pdf
│ ├── cn_cumm.png
│ ├── cn_cumm.svg
│ ├── count_amplicons.pdf
│ ├── count_amplicons.png
│ ├── count_amplicons.svg
│ ├── count_amplicons_nolegend.pdf
│ ├── count_amplicons_nolegend.png
│ ├── count_amplicons_nolegend.svg
│ ├── fragments_size.pdf
│ ├── fragments_size.png
│ ├── fragments_size.svg
│ ├── fragments_size_bytopology.pdf
│ ├── fragments_size_bytopology.png
│ ├── fragments_size_bytopology.svg
│ ├── fragments_size_bytopology_cumm.pdf
│ ├── fragments_size_bytopology_cumm.png
│ ├── fragments_size_bytopology_cumm.svg
│ ├── fragments_size_bytopology_nolegend.pdf
│ ├── fragments_size_bytopology_nolegend.png
│ ├── fragments_size_bytopology_nolegend.svg
│ ├── fragments_size_bytopology_nolegend_notitle.pdf
│ ├── fragments_size_bytopology_nolegend_notitle.png
│ ├── fragments_size_bytopology_nolegend_notitle.svg
│ ├── fragments_size_bytopology_signif.pdf
│ ├── fragments_size_bytopology_signif.png
│ ├── fragments_size_bytopology_signif.svg
│ ├── fragments_size_bytopology_signif_nolegend.pdf
│ ├── fragments_size_bytopology_signif_nolegend.png
│ ├── fragments_size_bytopology_signif_nolegend.svg
│ ├── fragments_size_bytopology_signif_nolegend_notitle.pdf
│ ├── fragments_size_bytopology_signif_nolegend_notitle.png
│ ├── fragments_size_bytopology_signif_nolegend_notitle.svg
│ ├── fragments_size_notitle.pdf
│ ├── fragments_size_notitle.png
│ ├── fragments_size_notitle.svg
│ ├── length_ecDNA_bytopology.pdf
│ ├── length_ecDNA_bytopology.png
│ ├── length_ecDNA_bytopology.svg
│ ├── length_ecDNA_bytopology_cumm.pdf
│ ├── length_ecDNA_bytopology_cumm.png
│ ├── length_ecDNA_bytopology_cumm.svg
│ ├── length_ecDNA_bytopology_hist.pdf
│ ├── length_ecDNA_bytopology_hist.png
│ ├── length_ecDNA_bytopology_hist.svg
│ ├── length_ecDNA_hist.pdf
│ ├── length_ecDNA_hist.png
│ ├── length_ecDNA_hist.svg
│ ├── length_vs_cn.pdf
│ ├── length_vs_cn.png
│ ├── length_vs_cn.svg
│ ├── length_vs_cn_celllines.pdf
│ ├── length_vs_cn_celllines.png
│ ├── length_vs_cn_celllines.svg
│ ├── length_vs_cn_withlegend.pdf
│ ├── length_vs_cn_withlegend.png
│ └── length_vs_cn_withlegend.svg
├── SupplFigS1
│ ├── plot_CHP212.html
│ └── plot_CHP212_assembly_comparison.html
├── SupplFigS2
│ └── TR14_bandage_shasta_amplicons.png
├── SupplFigS4_S3
│ ├── plot_CHP212_assembly_comparison.html
│ ├── plot_STA-NB-10DM_assembly_comparison.html
│ ├── plot_TR14_assembly_comparison.html
│ └── plot_TR14_assembly_comparison.pdf
├── SupplFigS6_lasso
│ ├── 4_Decoil_Dev_2.ipynb
│ └── figures
│ ├── lasso_experiment_overlap.pdf
│ ├── lasso_experiment_overlap.png
│ ├── lasso_experiment_overlap.svg
│ ├── lasso_experiment_overlap_subcircles.pdf
│ ├── lasso_experiment_overlap_subcircles.png
│ └── lasso_experiment_overlap_subcircles.svg
├── SupplFigS8_runtime
│ ├── Figures
│ │ ├── CPUTime_Min_real.pdf
│ │ ├── CPUTime_Min_real.png
│ │ ├── CPUTime_Min_simulation.pdf
│ │ ├── CPUTime_Min_simulation.png
│ │ ├── Elapsed_Min_real.pdf
│ │ ├── Elapsed_Min_real.png
│ │ ├── Elapsed_Min_simulation.pdf
│ │ ├── Elapsed_Min_simulation.png
│ │ ├── MaxRss_GB_real.pdf
│ │ ├── MaxRss_GB_real.png
│ │ ├── MaxRss_GB_simulation.pdf
│ │ └── MaxRss_GB_simulation.png
│ ├── Figures-Backup
│ │ ├── CPUTime_Min_real.png
│ │ ├── CPUTime_Min_simulation.png
│ │ ├── Elapsed_Min_real.png
│ │ ├── Elapsed_Min_simulation.png
│ │ ├── MaxRss_GB_real.png
│ │ └── MaxRss_GB_simulation.png
│ ├── Runtime.ipynb
│ ├── runtime_metrics_all.txt
│ ├── runtime_metrics_mapping_cresil.txt
│ └── runtime_metrics_table.txt
└── SupplFigS9
└── 13_FilterSimilarCycles
├── count_simple_circles_overlapping.pdf
├── count_simple_circles_overlapping.png
└── count_simple_circles_overlapping.svg