GitHub

Tutorials

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

Getting Started

Core Workflow Tutorials

  1. 01 Data Acquisition - Downloading and simulating sequence data
  2. 02 Quality Control - Quality assessment and filtering
  3. 03 K-mer Analysis - K-mer counting and spectrum analysis
  4. 04 Genome Assembly - Assembly algorithms and execution
  5. 05 Assembly Validation - Quality metrics and validation
  6. 06 Gene Annotation - Gene prediction and annotation
  7. 07 Comparative Genomics - Pangenome and phylogenetic analysis
  8. 08 Tool Integration - Working with external bioinformatics tools

Specialized Topics

Graph Types and Assembly Methods

4b. 04 Graph Type Tutorials - Overview of different graph structures

Round-Trip Examples

09a. 09 Round Trip 01: String Graphs - String graph construction and traversal 09b. 09 Round Trip 02: N-gram to String - Converting between representations 09c. 09 Round Trip 03: FASTA Sequences - Working with FASTA format 09d. 09 Round Trip 04: K-mer to Sequence - K-mer graph reconstruction 09e. 09 Round Trip 05: FASTQ Graphs - Quality-aware graph construction 09f. 09 Round Trip 06: Qualmer Graphs - Quality-weighted k-mer graphs

Advanced Topics

  1. 10 Viroid Assembly Workflow - Complete workflow for circular viral genomes
  2. 11 Reduced Amino Acid Alphabets - Reduced alphabet encodings and analysis
  3. 12 CoverM Coverage - Coverage profiling and reporting
  4. 13 Rhizomorph Assembly - Rhizomorph assembly workflows

14a. 14 Binning Workflow - Binning and post-binning workflows 14b. 14 Mash Classification - Mash sketching and screening

  1. 15 Round Trip Benchmarking - Reference download and simulation harness
  2. 16 UN Corpus Ngram vs Token Graphs - Graph comparisons on UN corpus data
  3. 17 Viroid Sketch Round Trip - BLAST DB export, sketching, and validation
  4. 18 Advanced Assembly Theory and Practice - Deep dive into assembly algorithms

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