Tutorials

The following tutorials aim to cover the common bioinformatics workflows from data acquisition to comparative genomics.

Getting Started

• Assembly in 5 Minutes - Quick introduction to genome assembly with Mycelia

Core Workflow Tutorials

1. Data Acquisition - Downloading and simulating sequence data
2. Quality Control - Quality assessment and filtering
3. K-mer Analysis - K-mer counting and spectrum analysis
4. Genome Assembly - Assembly algorithms and execution
5. Assembly Validation - Quality metrics and validation
6. Gene Annotation - Gene prediction and annotation
7. Comparative Genomics - Pangenome and phylogenetic analysis
8. Tool Integration - Working with external bioinformatics tools

Specialized Topics

Graph Types and Assembly Methods

• Graph Type Tutorials - Overview of different graph structures

Round-Trip Examples

1. String Graphs - String graph construction and traversal
2. N-gram to String - Converting between representations
3. FASTA Sequences - Working with FASTA format
4. K-mer to Sequence - K-mer graph reconstruction
5. FASTQ Graphs - Quality-aware graph construction
6. Qualmer Graphs - Quality-weighted k-mer graphs

Advanced Topics

• Advanced Assembly Theory and Practice - Deep dive into assembly algorithms
• Viroid Assembly Workflow - Complete workflow for circular viral genomes

Running Tutorials

All tutorials are executable Julia scripts. To run a tutorial:

import Mycelia
include("tutorials/01_data_acquisition.jl")

Or run all tutorials:

include("tutorials/run_all_tutorials.jl")

Next Steps

• Review the API Reference for detailed function documentation
• See Getting Started for installation and basic usage
• Check Examples for common workflow patterns