├── Figures_README ├── Circular_genome_start.png ├── Collapsed_repeat.png ├── Collapsed_tandem_repeat_case1.png ├── Collapsed_tandem_repeat_case2.png ├── Deletion.png ├── Duplication.png ├── Gap.png ├── IGV_query_additional.png ├── IGV_query_blocks.png ├── IGV_query_snps.png ├── IGV_query_struct.png ├── IGV_ref_additional.png ├── IGV_ref_blocks.png ├── IGV_ref_snps.png ├── IGV_ref_struct.png ├── Inserted_gap.png ├── Insertion.png ├── Inversion.png ├── Relocation_1.png ├── Relocation_2.png ├── Relocation_inserted_gap.png ├── Relocation_inserted_gap_2.png ├── Relocation_insertion.png ├── Relocation_insertion_2.png ├── Relocation_insertion_mix.png ├── Relocation_insertion_mix_2.png ├── Relocation_overlap.png ├── Relocation_overlap_2.png ├── Reshuffling.png ├── Substitution.png ├── Tandem_duplication_case1.png ├── Tandem_duplication_case2.png ├── Translocation_1.png ├── Translocation_2.png ├── Translocation_inserted_gap.png ├── Translocation_inserted_gap_2.png ├── Translocation_insertion.png ├── Translocation_insertion_2.png ├── Translocation_insertion_mix.png ├── Translocation_insertion_mix_2.png ├── Translocation_overlap.png ├── Translocation_overlap_2.png ├── Unaligned_beginning.png ├── Unaligned_end.png ├── igv_example1.png ├── ref_blocks.png ├── types_of_differences.png └── workflow.png ├── LICENSE ├── MANIFEST.in ├── README.md ├── nucdiff ├── __init__.py ├── __version__.py ├── class_errors.py ├── class_interv_coord.py ├── class_nucmer.py ├── find_errors.py ├── general.py ├── generate_output.py ├── initial_preparation.py ├── nucdiff.py ├── ref_coord.py └── statistics.py └── setup.py /Figures_README/Circular_genome_start.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uio-cels/NucDiff/HEAD/Figures_README/Circular_genome_start.png -------------------------------------------------------------------------------- /Figures_README/Collapsed_repeat.png: 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