API Documentation

Welcome to the Mycelia API documentation! This guide organizes both implemented functions and planned features by biological workflows. Mycelia provides substantial functionality for bioinformatics analysis with extensive tool integration, while continuing to expand with experimental algorithms and additional features.

Quick Start

New to Mycelia? Start with our workflow-based guides:

• Basic Workflows - Common analysis patterns
• Function Index - Alphabetical function list
• Parameter Guide - Common parameters explained

By Workflow Stage

Follow the typical bioinformatics analysis workflow:

• Data Acquisition & Simulation
• • Overview
  • Common Workflows
  • Public Database Downloads
  • Data Simulation
  • Data Validation (Planned)
  • Metadata Management (Planned)
  • Performance Considerations
  • Common Issues and Solutions
  • Related Functions
  • See Also
• Quality Control & Preprocessing
• • Overview
  • Common Workflows
  • Quality Assessment
  • Preprocessing and Filtering
  • Contamination Detection
  • Quality Metrics and Reporting
  • Specialized Quality Control
  • Visualization and Plotting
  • Performance Optimization
  • Common Issues and Solutions
  • Related Functions
  • Related Workflows
  • See Also
• Sequence Analysis & K-mers
• • Overview
  • Common Workflows
  • K-mer Counting
  • K-mer Frequency Analysis
  • Error Detection and Correction (Planned)
  • Sequence Composition Analysis (Planned)
  • Memory-Efficient Processing
  • Comparative K-mer Analysis (Planned)
  • Visualization and Reporting
  • Performance Considerations
  • Common Issues and Solutions
  • Related Functions
  • See Also

1. Data Acquisition & Simulation

Download genomic data from public databases and simulate synthetic datasets for testing.

Working Functions: download_genome_by_accession, simulate_pacbio_reads, simulate_nanopore_reads

2. Quality Control & Preprocessing

Assess and improve sequencing data quality before analysis.

Working Functions: analyze_fastq_quality, calculate_gc_content, assess_duplication_rates, qc_filter_short_reads_fastp, qc_filter_long_reads_filtlong, trim_galore_paired Planned: filter_by_quality, per-base quality visualization

3. Sequence Analysis & K-mers

Analyze sequence composition, count k-mers, and extract genomic features.

Working Functions: count_canonical_kmers, jaccard_distance, kmer_counts_to_js_divergence Planned: kmer_frequency_spectrum, estimate_genome_size

4. Genome Assembly (planned)

Assemble genomes from sequencing reads using various approaches.

Working Functions: assemble_metagenome_megahit, assemble_metagenome_metaspades (external tools) Experimental: Graph-based assembly framework Planned: assemble_genome, polish_assembly

5. Assembly Validation

Validate and assess the quality of genome assemblies.

Working Functions: assess_assembly_quality, validate_assembly, run_quast, run_busco, run_mummer, CheckM/CheckM2 integration Planned: Mauve integration

6. Gene Annotation

Predict genes and assign functional annotations.

Working Functions: Pyrodigal, BLAST+, MMSeqs2, TransTerm, tRNAscan-SE, MLST integrations Planned: GO term analysis, Reactome pathway analysis, PDB integration via UniRef annotations

7. Comparative Genomics (planned)

Compare genomes, build pangenomes, and construct phylogenetic trees.

Working Functions: analyze_pangenome_kmers, build_genome_distance_matrix Planned: construct_phylogeny, calculate_synteny

8. Visualization & Reporting

Create plots, figures, and reports for analysis results.

Working Functions: plot_kmer_frequency_spectra, visualize_genome_coverage, plot_embeddings, plot_taxa_abundances, coverage plots, taxonomic visualizations Planned: Per-base quality plots, assembly statistics visualization, phylogenetic tree plotting

By Data Type

Working with specific file formats and data structures:

<!– Data type documentation planned for future releases

• FASTA and FASTQ Data Types
• • Reading Files
  • Writing Files
  • Related Documentation

–>

FASTA/FASTQ Files (planned)

Reading, writing, and manipulating sequence files.

Assembly Files (planned)

Working with contigs, scaffolds, and assembly statistics.

Annotation Files (planned)

Handling GFF3, GenBank, and other annotation formats.

Alignment Files (planned)

Processing BAM/SAM files and alignment results.

Phylogenetic Trees (planned)

Tree construction, manipulation, and visualization.

By Analysis Goal

Cross-cutting concerns and specific use cases:

• Basic Workflows
• • Overview
  • Workflow 1: Bacterial Genome Assembly (Planned API Design)
  • Workflow 2: Comparative Genomics Analysis
  • Workflow 3: Quality Control Pipeline
  • Workflow 4: Assembly Optimization
  • Workflow 5: Contamination Detection and Removal
  • Error Handling and Robustness
  • Performance Optimization
  • Next Steps
  • See Also
• Advanced Usage Examples
• • Performance Optimization
  • Advanced Workflows
  • Related Documentation
• Function Index
• • A
  • B
  • C
  • D
  • E
  • F
  • G
  • H
  • I
  • K
  • N
  • P
  • R
  • S
  • V
  • W
  • Function Categories
  • Search Tips
  • See Also
• Parameter Guide
• • Overview
  • File Path Parameters
  • Quality Control Parameters
  • K-mer Analysis Parameters
  • Assembly Parameters
  • Comparative Genomics Parameters
  • Performance Parameters
  • File Format Parameters
  • Error Handling Parameters
  • Common Parameter Patterns
  • Parameter Validation
  • Troubleshooting Common Issues
  • See Also

Basic Workflows

Complete examples for common analysis tasks.

Advanced Usage

Complex workflows and optimization techniques.

Function Index

Alphabetical listing of all functions with brief descriptions.

Parameter Guide

Common parameters and their usage across functions.

Finding What You Need

By Task

• "I want to assemble a genome" → Genome Assembly (planned)
• "I need to validate my assembly" → Assembly Validation (planned)
• "I want to compare genomes" → Comparative Genomics (planned)
• "I need to check data quality" → Quality Control

By Data Type

• "I have FASTQ files" → FASTA/FASTQ Files (planned)
• "I have assembly contigs" → Assembly Files (planned)
• "I have gene annotations" → Annotation Files (planned)

By Experience Level

• Beginner → Basic Workflows
• Intermediate → Workflow-specific guides
• Advanced → Advanced Usage

Integration with Tutorials

This API documentation integrates with the tutorial system:

• Tutorials show complete workflows with explanation
• API docs provide detailed function reference
• Examples bridge the gap with focused use cases

For hands-on learning, see the Tutorials which use these functions in complete bioinformatics workflows.

This documentation is automatically generated from function docstrings and organized for biological workflows. Functions are tested through the tutorial system to ensure accuracy.