├── .github └── workflows │ └── nanopolish.yaml ├── .gitignore ├── .gitmodules ├── .travis.yml ├── DEVELOPERS.md ├── Dockerfile ├── Dockerfile-arm ├── LICENSE ├── Makefile ├── README.md ├── docs ├── Makefile └── source │ ├── _static │ ├── nanopolish-workflow.png │ └── quickstart_methylation_results.png │ ├── conf.py │ ├── debug.rst │ ├── index.rst │ ├── installation.rst │ ├── manual.rst │ ├── quickstart_call_methylation.rst │ ├── quickstart_consensus.rst │ ├── quickstart_eventalign.rst │ └── quickstart_polya.rst ├── etc ├── htslib_config.h └── r9-models │ ├── r9.4_450bps.cpg.6mer.template.model │ ├── r9.4_450bps.gpc.6mer.template.model │ ├── r9.4_450bps.nucleotide.5mer.template.model │ ├── r9.4_450bps.nucleotide.6mer.template.model │ ├── r9.4_70bps.u_to_t_rna.5mer.template.model │ ├── r9_250bps.cpg.6mer.template.model │ ├── r9_250bps.nucleotide.5mer.complement.pop1.model │ ├── r9_250bps.nucleotide.5mer.complement.pop2.model │ ├── r9_250bps.nucleotide.5mer.template.model │ ├── r9_250bps.nucleotide.6mer.complement.pop1.model │ ├── r9_250bps.nucleotide.6mer.complement.pop2.model │ └── r9_250bps.nucleotide.6mer.template.model ├── scripts ├── calculate_methylation_frequency.py ├── compare_methylation.py ├── consensus-preprocess.pl ├── consensus.make ├── convert_all_models.py ├── convert_model_to_header.py ├── dropmodel.py ├── extract_reads_aligned_to_region.py ├── import_ont_model.py ├── import_ont_models_from_dir.sh ├── nanopolish_makerange.py ├── nanopolish_merge.py ├── polya_training │ ├── dump_signal.py │ ├── environment.yml │ ├── hmmplot.py │ ├── retrain_emission.py │ └── workflow.md ├── reestimate_polya_emissions.py └── requirements.txt ├── src ├── alignment │ ├── nanopolish_alignment_db.cpp │ ├── nanopolish_alignment_db.h │ ├── nanopolish_anchor.cpp │ ├── nanopolish_anchor.h │ ├── nanopolish_eventalign.cpp │ └── nanopolish_eventalign.h ├── basemods │ ├── nanopolish_basemods.cpp │ └── nanopolish_basemods.h ├── builtin_models │ ├── r9_250bps_cpg_6mer_template_model.inl │ ├── r9_250bps_nucleotide_5mer_complement_pop1_model.inl │ ├── r9_250bps_nucleotide_5mer_complement_pop2_model.inl │ ├── r9_250bps_nucleotide_5mer_template_model.inl │ ├── r9_250bps_nucleotide_6mer_complement_pop1_model.inl │ ├── r9_250bps_nucleotide_6mer_complement_pop2_model.inl │ ├── r9_250bps_nucleotide_6mer_template_model.inl │ ├── r9_4_450bps_cpg_6mer_template_model.inl │ ├── r9_4_450bps_dam_6mer_template_model.inl │ ├── r9_4_450bps_dcm_6mer_template_model.inl │ ├── r9_4_450bps_gpc_6mer_template_model.inl │ ├── r9_4_450bps_nucleotide_5mer_template_model.inl │ ├── r9_4_450bps_nucleotide_6mer_template_model.inl │ └── r9_4_70bps_u_to_t_rna_5mer_template_model.inl ├── common │ ├── alg.hpp │ ├── fs_support.cpp │ ├── fs_support.hpp │ ├── logger.hpp │ ├── logsum.cpp │ ├── logsum.h │ ├── logsumset.hpp │ ├── nanopolish_alphabet.cpp │ ├── nanopolish_alphabet.h │ ├── nanopolish_bam_processor.cpp │ ├── nanopolish_bam_processor.h │ ├── nanopolish_bam_utils.cpp │ ├── nanopolish_bam_utils.h │ ├── nanopolish_common.cpp │ ├── nanopolish_common.h │ ├── nanopolish_iupac.cpp │ ├── nanopolish_iupac.h │ ├── nanopolish_klcs.cpp │ ├── nanopolish_klcs.h │ ├── nanopolish_matrix.h │ ├── nanopolish_variant.cpp │ ├── nanopolish_variant.h │ ├── profiler.h │ └── progress.h ├── hmm │ ├── invgauss.hpp │ ├── nanopolish_duration_model.cpp │ ├── nanopolish_duration_model.h │ ├── nanopolish_emissions.h │ ├── nanopolish_hmm_input_sequence.h │ ├── nanopolish_profile_hmm.cpp │ ├── nanopolish_profile_hmm.h │ ├── nanopolish_profile_hmm_r7.cpp │ ├── nanopolish_profile_hmm_r7.h │ ├── nanopolish_profile_hmm_r7.inl │ ├── nanopolish_profile_hmm_r9.cpp │ ├── nanopolish_profile_hmm_r9.h │ ├── nanopolish_profile_hmm_r9.inl │ ├── nanopolish_transition_parameters.cpp │ └── nanopolish_transition_parameters.h ├── io │ ├── nanopolish_fast5_io.cpp │ ├── nanopolish_fast5_io.h │ ├── nanopolish_fast5_loader.cpp │ ├── nanopolish_fast5_loader.h │ ├── nanopolish_fast5_processor.cpp │ └── nanopolish_fast5_processor.h ├── main │ └── nanopolish.cpp ├── nanopolish_call_methylation.cpp ├── nanopolish_call_methylation.h ├── nanopolish_call_variants.cpp ├── nanopolish_call_variants.h ├── nanopolish_detect_polyi.cpp ├── nanopolish_detect_polyi.h ├── nanopolish_fast5_check.cpp ├── nanopolish_fast5_check.h ├── nanopolish_haplotype.cpp ├── nanopolish_haplotype.h ├── nanopolish_index.cpp ├── nanopolish_index.h ├── nanopolish_methyltrain.cpp ├── nanopolish_methyltrain.h ├── nanopolish_phase_reads.cpp ├── nanopolish_phase_reads.h ├── nanopolish_polya_estimator.cpp ├── nanopolish_polya_estimator.h ├── nanopolish_raw_loader.cpp ├── nanopolish_raw_loader.h ├── nanopolish_read_db.cpp ├── nanopolish_read_db.h ├── nanopolish_scorereads.cpp ├── nanopolish_scorereads.h ├── nanopolish_squiggle_read.cpp ├── nanopolish_squiggle_read.h ├── nanopolish_train_poremodel_from_basecalls.cpp ├── nanopolish_train_poremodel_from_basecalls.h ├── 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