├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── README.md ├── code_of_conduct.md ├── extern └── local_kmer_models │ ├── r10_180mv_450bps_9mer │ └── template_r10_9mer.model │ └── uncalled_r1041_model_only_means.txt ├── gitfigures ├── overview.png ├── rawhash-preview.png └── rawsamble.png ├── src ├── Makefile ├── bseq.c ├── bseq.h ├── chain.h ├── dtw.cpp ├── dtw.h ├── hdf5_tools.hpp ├── hit.c ├── kalloc.c ├── kalloc.h ├── ketopt.h ├── khash.h ├── krmq.h ├── kseq.h ├── ksort.h ├── kthread.c ├── kthread.h ├── lchain.c ├── main.cpp ├── rawhash.h ├── revent.c ├── revent.h ├── rh_kvec.h ├── rindex.c ├── rindex.h ├── rmap.cpp ├── rmap.h ├── roptions.c ├── roptions.h ├── rseed.c ├── rseed.h ├── rsig.c ├── rsig.h ├── rsketch.c ├── rsketch.h ├── rutils.c ├── rutils.h ├── sequence_until.c └── sequence_until.h └── test ├── README.md ├── data ├── README.md ├── contamination │ └── generate_fast5_files.sh ├── download_d1_sars-cov-2_r94.sh ├── download_d2_ecoli_r94.sh ├── download_d3_yeast.sh ├── download_d4_green_algae.sh ├── download_d5_human_na12878.sh ├── download_d6_ecoli_r10.4.sh ├── download_d7_saureus_r104.sh ├── download_d9_ecoli_r1041.sh ├── random_community │ ├── 0_generate_random_ids.sh │ └── read_ids.txt └── relative_abundance │ ├── generate_fast5_files.sh │ ├── generate_ref.sh │ └── list.txt ├── evaluation ├── README.md ├── contamination │ ├── README.md │ ├── comparison │ │ ├── 0_run.sh │ │ ├── 1_generate_results.sh │ │ └── 2_output_results.sh │ ├── run_rawhash.sh │ ├── run_rawhash2.sh │ ├── run_sigmap.sh │ └── run_uncalled.sh ├── rawsamble │ ├── README.md │ ├── d2_ecoli_r94 │ │ ├── README.md │ │ └── run_rawhash2.sh │ ├── d3_yeast_r94 │ │ ├── README.md │ │ └── run_rawhash2.sh │ ├── d4_green_algae_r94 │ │ ├── README.md │ │ └── run_rawhash2.sh │ └── d9_ecoli_r1041 │ │ ├── README.md │ │ └── run_rawhash2.sh ├── read_mapping │ ├── README.md │ ├── d1_sars-cov-2_r94 │ │ ├── README.md │ │ ├── comparison │ │ │ ├── 0_run.sh │ │ │ ├── 1_generate_results.sh │ │ │ └── 2_output_results.sh │ │ ├── profile_rawhash2.sh │ │ ├── run_minimap2.sh │ │ ├── run_rawhash.sh │ │ ├── run_rawhash2.sh │ │ ├── run_sigmap.sh │ │ └── run_uncalled.sh │ ├── d2_ecoli_r94 │ │ ├── README.md │ │ ├── comparison │ │ │ ├── 0_run.sh │ │ │ ├── 1_generate_results.sh │ │ │ └── 2_output_results.sh │ │ ├── profile_rawhash2.sh │ │ ├── run_minimap2.sh │ │ ├── run_rawhash.sh │ │ ├── run_rawhash2.sh │ │ ├── run_rawhash2_pod5.sh │ │ ├── run_rawhash2_slow5.sh │ │ ├── run_rawhash_pod5.sh │ │ ├── run_sigmap.sh │ │ └── run_uncalled.sh │ ├── d3_yeast_r94 │ │ ├── README.md │ │ ├── comparison │ │ │ ├── 0_run.sh │ │ │ ├── 1_generate_results.sh │ │ │ └── 2_output_results.sh │ │ ├── profile_rawhash2.sh │ │ ├── run_minimap2.sh │ │ ├── run_rawhash.sh │ │ ├── run_rawhash2.sh │ │ ├── run_rawhash2_pod5.sh │ │ ├── run_rawhash2_slow5.sh │ │ ├── run_rawhash_pod5.sh │ │ ├── run_sigmap.sh │ │ └── run_uncalled.sh │ ├── d4_green_algae_r94 │ │ ├── README.md │ │ ├── comparison │ │ │ ├── 0_run.sh │ │ │ ├── 1_generate_results.sh │ │ │ └── 2_output_results.sh │ │ ├── profile_rawhash2.sh │ │ ├── run_minimap2.sh │ │ ├── run_rawhash.sh │ │ ├── run_rawhash2.sh │ │ ├── run_sigmap.sh │ │ └── run_uncalled.sh │ ├── d5_human_na12878_r94 │ │ ├── README.md │ │ ├── comparison │ │ │ ├── 0_run.sh │ │ │ ├── 1_generate_results.sh │ │ │ └── 2_output_results.sh │ │ ├── profile_rawhash2.sh │ │ ├── run_minimap2.sh │ │ ├── run_rawhash.sh │ │ ├── run_rawhash2.sh │ │ ├── run_sigmap.sh │ │ └── run_uncalled.sh │ ├── d6_ecoli_r104 │ │ ├── README.md │ │ ├── comparison │ │ │ ├── 0_run.sh │ │ │ ├── 1_generate_results.sh │ │ │ └── 2_output_results.sh │ │ ├── profile_rawhash.sh │ │ ├── run_minimap2.sh │ │ └── run_rawhash2.sh │ └── d7_saureus_r104 │ │ ├── comparison │ │ ├── 0_run.sh │ │ ├── 1_generate_results.sh │ │ └── 2_output_results.sh │ │ ├── profile_rawhash.sh │ │ ├── run_minimap2.sh │ │ └── run_rawhash2.sh └── relative_abundance │ ├── README.md │ ├── comparison │ ├── 0_run.sh │ ├── 1_generate_results.sh │ └── 2_output_results.sh │ ├── run_minimap2.sh │ ├── run_rawhash.sh │ ├── run_rawhash2.sh │ ├── run_sigmap.sh │ ├── run_uncalled.sh │ └── sequenceuntil │ ├── README.md │ ├── output.sh │ ├── run_rawhash2.sh │ └── simulate │ ├── 1_shuffle.sh │ └── 2_output.sh ├── figures ├── figures.pptx ├── profiling.pdf ├── profiling │ ├── plot.py │ ├── profiling.csv │ └── profiling.pdf ├── sequenced_bases.pdf ├── sequenced_bases │ ├── plot.py │ ├── sequenced_bases.csv │ └── sequenced_bases.pdf ├── sequenced_chunks.pdf ├── sequenced_chunks │ ├── plot.py │ ├── sequenced_chunks.csv │ └── sequenced_chunks.pdf ├── throughput.pdf ├── throughput │ ├── plot.py │ ├── throughput.csv │ └── throughput.pdf ├── time_per_read.pdf └── time_per_read │ ├── mean_time.csv │ ├── mean_time.pdf │ └── plot.py └── scripts ├── analyze_gfa.sh ├── compare_pafs.py ├── compare_relative_pafs.py ├── evaluate_gfa.py ├── pafstats.py ├── run_minimap2.sh ├── run_minimap2_multimap.sh ├── run_rawhash.sh ├── 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