├── .gitmodules ├── LICENSE ├── README.md ├── clean.sh └── src ├── alignment_filter.py ├── analyze_bac_subgraph.sh ├── analyze_subgraph.sh ├── assign_coverage.py ├── canu_launch ├── canu.sh ├── examples.sh ├── fix_errors.sh ├── master_trim.sh ├── on_init_complete.sh ├── on_primary_complete.sh └── rebuild_seqstore.sh ├── chm13_analysis ├── extract_all_bac_subgraphs.sh ├── extract_broken_bac_subgraphs.sh ├── get_intermediate.sh ├── icarus_gaps │ ├── Snakefile │ └── launch.sh ├── rebuild_seqstore.sh ├── run_icarus.sh ├── run_subgraphs.sh └── uplift_paths.sh ├── compact_gfa.py ├── consensus ├── Snakefile ├── backbone_analysis.py ├── cluster.json ├── config.yaml ├── consensus.sh ├── join_ctgs.py ├── launch.sh ├── meta_consensus.sh ├── rename_reads.py ├── resolve_layouts.sh └── translate_backbone_layout.py ├── contig_processing ├── align.sh ├── augment_node_list.sh ├── cmd.sh ├── contig_info.py ├── extract_contigs.py ├── gap_patch.py ├── gap_patch.sh ├── homopolymer_compress.py ├── length_filter.py ├── master_patch.sh ├── merge_reads.py ├── patch_from_bed.sh └── telomere_patch.py ├── coord_uplift.py ├── deadends.py ├── extract_cov_micro.sh ├── extract_cov_mikko.sh ├── fix_node_info.sh ├── inject_coverage.py ├── inject_sequence.py ├── join_segments.py ├── node_coverage.sh ├── normalize_paf.py ├── pipe ├── Snakefile ├── build_graph.sh ├── chr_analysis.sh ├── cluster.json ├── config.yaml ├── final_simplif.sh ├── launch.sh ├── launch_local.sh ├── mashmap.sh ├── pipe.sh └── simplif.sh ├── preprocess_gfa.py ├── process_simplified.sh ├── read_alignment ├── Snakefile ├── cluster.json ├── config.yaml ├── graphalign.sh ├── launch.sh └── winnowmap.sh ├── requirements.txt ├── resolution ├── checkPaths.sh ├── ga_ont.sh ├── post_process_gaf.py ├── reshuffle.py ├── selectReads.sh ├── subset_winnowmap_ont.sh ├── summarizeGap.sh ├── use_ont.sh └── winnowmap_ont.sh ├── resolve_layouts.py └── rlCutoff.py /.gitmodules: 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