Complete API Surface
This page is generated directly from the package docstrings so every documented function, type, and constant available in the current codebase is visible in one place. Use this as a coverage checklist when adding new functionality: if a symbol is missing here, it either lacks a docstring or has not been included in the documentation build pipeline.
Index of All Documented Symbols
Mycelia.GraphModeMycelia.QualmerMycelia.QualmerEdgeDataMycelia.QualmerVertexDataMycelia.StrandOrientationMycelia.analyze_fastq_qualityMycelia.assemble_genomeMycelia.assess_assembly_qualityMycelia.assess_duplication_ratesMycelia.build_kmer_graph_nextMycelia.build_qualmer_graphMycelia.calculate_gc_contentMycelia.collapse_unbranching_pathsMycelia.convert_sequenceMycelia.count_canonical_kmersMycelia.count_kmersMycelia.download_genome_by_accessionMycelia.download_sra_dataMycelia.estimate_genome_size_from_kmersMycelia.fasta_list_to_dense_kmer_countsMycelia.fasta_list_to_sparse_kmer_countsMycelia.fasterq_dump_parallelMycelia.find_connected_componentsMycelia.get_qualmer_statisticsMycelia.jaccard_distanceMycelia.jellyfish_counts_to_kmer_frequency_histogramMycelia.joint_qualmer_probabilityMycelia.kmer_counts_to_js_divergenceMycelia.load_kmer_resultsMycelia.ncbi_genome_download_accessionMycelia.ngramsMycelia.open_fastxMycelia.phred_to_probabilityMycelia.plot_embeddingsMycelia.plot_kmer_frequency_spectraMycelia.plot_ngram_graphMycelia.plot_taxa_abundancesMycelia.position_wise_joint_probabilityMycelia.prefetch_sra_runsMycelia.qc_filter_long_reads_fastplongMycelia.qc_filter_long_reads_filtlongMycelia.qc_filter_short_reads_fastpMycelia.qualmer_correctness_probabilityMycelia.qualmers_canonicalMycelia.qualmers_fwMycelia.qualmers_unambiguousMycelia.qualmers_unambiguous_canonicalMycelia.random_fasta_recordMycelia.run_buscoMycelia.run_coverm_contigMycelia.run_coverm_genomeMycelia.run_mummerMycelia.run_quastMycelia.save_kmer_resultsMycelia.simulate_illumina_readsMycelia.simulate_nanopore_readsMycelia.simulate_pacbio_readsMycelia.string_to_ngram_graphMycelia.trim_galore_pairedMycelia.validate_assemblyMycelia.visualize_genome_coverageMycelia.write_fastaMycelia.write_fastq
Detailed Reference (auto-generated)
Keeping the API Complete
- Implemented, documented functions will appear above. Add docstrings in the source files to include new symbols automatically.
- Experimental or deprecated functions are included for transparency; mark them in their docstrings accordingly.
- Planned functions should be captured in the Function Index and the Workflow & Tool Map until they are implemented and documented.