Mycelia Documentation

An experimental Julia package for bioinformatics and computational biology

Mycelia is a research-oriented package exploring best-practice methodologies for pan-multi-omics analysis and graph-based assembly with quality-aware sequence processing. Currently in early development, it provides both experimental algorithms and integrations with established bioinformatics tools.

Quick Start

New to Mycelia? Start with our Getting Started Guide to install the package and complete your first genomic analysis in minutes.

Key Features & Research Areas

Production-Ready Features

• Third-Party Assembly Tools: Stable wrappers for 15+ established assemblers including MEGAHIT, SPAdes, Flye, hifiasm, Canu, Unicycler, Velvet, and others
• Sequence Processing: FASTA/FASTQ I/O and read simulation (Illumina, PacBio, Nanopore)
• K-mer Analysis: Canonical k-mer counting and distance metrics
• Quality Control Tools: Integration with fastp, filtlong, trim_galore
• Assembly Validation: QUAST, BUSCO, CheckM/CheckM2, MUMmer integration
• Annotation Tools: Pyrodigal, BLAST+, MMSeqs2, TransTerm, tRNAscan-SE, MLST integration
• HPC Support: SLURM job submission and rclone cloud storage integration

Experimental/Research Features

• Internal Assembly Algorithms: Graph-based approaches with quality awareness (6-graph hierarchy)
• Intelligent Assembly: Self-optimizing parameter selection and k-mer progression
• Qualmer Analysis: Quality-aware k-mer assembly and probabilistic path selection
• Reinforcement Learning Assembly: ML-guided assembly optimization (proof-of-concept)
• Pangenome Analysis: K-mer based comparative genomics

Planned Features

• Annotation: Gene prediction and functional annotation
• Phylogenetics: Tree construction from pangenome data
• Visualization: Interactive plots for genomic data

Documentation Contents

• Getting Started with Mycelia
• • What is Mycelia?
  • Prerequisites
  • Installation
  • Your First Analysis
  • What's Next?
  • Getting Help
  • Memory and Performance
  • Contributing
• Bioinformatics Concepts and Tools
• • Table of Contents
  • Workflow Overview
  • Data Acquisition
  • Quality Control
  • Sequence Analysis
  • Genome Assembly
  • Gene Annotation
  • Comparative Genomics
  • Phylogenetics
  • Tool Selection Guide
• Tutorials
• • Getting Started
  • Core Workflow Tutorials
  • Specialized Topics
  • Advanced Topics
  • Running Tutorials
  • Next Steps
• API Documentation
• • Quick Start
  • By Workflow Stage
  • By Data Type
  • By Analysis Goal
  • Finding What You Need
  • Integration with Tutorials
• Visualization Gallery
• • Overview
  • Data Quality & Preprocessing (Partially Implemented)
  • Sequence Analysis & K-mers (Partially Implemented)
  • Assembly Visualization (Planned)
  • Annotation & Gene Features (Planned)
  • Comparative Genomics (Partially Implemented)
  • Performance & Benchmarking (Planned)
  • Customization and Export
  • Gallery Organization
  • Interactive Examples
• Frequently Asked Questions
• • Table of Contents
  • Installation and Setup
  • Assembly Questions
  • Performance and Optimization
  • Data Formats and Compatibility
  • Error Messages and Troubleshooting
  • Comparison with Other Tools
  • Getting Help
• Contributing to Mycelia
• • Getting Started
  • Development Setup
  • Code Standards
  • Submitting Changes
  • Pull Request Guidelines
  • Questions?
  • Code of Conduct

Installation

Quick Install

import Pkg
Pkg.add(url="https://github.com/cjprybol/Mycelia.git")

Development Install

import Pkg
Pkg.develop(url="git@github.com:cjprybol/Mycelia.git")

For detailed installation instructions including HPC setup, see the Getting Started Guide.

Function Docstrings

For complete API documentation, see the API Reference section.