├── .gitignore ├── ARAlignDetect.py ├── AmpliconReconstructorOM.py ├── ContigAlignmentGraph.py ├── LICENSE.md ├── OMPathFinder.py ├── README.md ├── SegAligner ├── CMakeLists.txt ├── Makefile ├── SAHelper.cpp ├── SAHelper.h ├── SegAligner ├── SegAligner.cpp ├── SegAligner.h └── main.cpp ├── abstract_graph.py ├── align_to_candidate_path.py ├── bionanoUtil.py ├── bionano_samples.yaml ├── breakpoint_graph.py ├── cycles_file_to_fasta.py ├── generate_cmap.py ├── global_names.py ├── graph_to_bed.py ├── ref_genomes ├── GRCh37_DLE1.cmap ├── GRCh37_DLE1_key.txt ├── GRCh38_BspQI.cmap.gz ├── GRCh38_BspQI_key.txt ├── GRCh38_DLE1.cmap ├── GRCh38_DLE1_key.txt ├── hg19_BspQI.cmap.gz ├── hg19_BspQI_key.txt ├── hg19_DLE1.cmap └── hg19_DLE1_key.txt ├── ref_util.py ├── scripts ├── extract_cmap.py ├── inverse_aln_cycle_ids.py ├── profile_reconstruction.py ├── readclust.py ├── reverse_aln_file.py └── split_molecules.py └── test_files ├── GBM39_BSPQI_EXP_REFINEFINAL1.cmap ├── GBM39_amplicon1_graph.txt ├── 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