MetaGraph API Examples

This repository contains examples demonstrating how to use MetaGraph as a C++ library for working with annotated de Bruijn graphs.

Overview

MetaGraph is a tool for scalable construction and indexing of genome graphs and sequence-to-graph alignment. This repository provides practical examples of using MetaGraph's C++ API in your own applications.

Two Integration Approaches

This repository demonstrates two different ways to integrate MetaGraph into your CMake project:

1. add_subdirectory - Simple & Direct

Best for active development and simpler projects. MetaGraph is included as a git submodule.

📖 See subdirectory/README.md for full instructions.

2. ExternalProject_Add - Automatic & Isolated

Best for downloading MetaGraph from Git automatically with stricter build isolation.

📖 See ExternalProject/README.md for full instructions.

Repository Structure

metagraph-examples/
├── subdirectory/              # Example using add_subdirectory
│   ├── CMakeLists.txt
│   ├── README.md
│   └── metagraph/             # MetaGraph submodule
├── ExternalProject/           # Example using ExternalProject_Add
│   ├── CMakeLists.txt
│   └── README.md
├── examples/                  # Example programs (shared)
│   └── basic_query.cpp
├── data/                      # Test data
│   ├── graphs/                # Pre-built test graphs
│   ├── test_DNA_query.fa
│   └── test_DNA_sequences.fa
└── README.md                  # This file

Quick Start

Choose your preferred integration method and follow its README:

• subdirectory/README.md - For add_subdirectory approach
• ExternalProject/README.md - For ExternalProject_Add approach

Both examples include:

• Pre-built test data (DNA and Protein graphs)
• A convenience target: run make run_example to execute with test data automatically
• Detailed build and usage instructions in their respective READMEs

What's Included

Example Code (examples/basic_query.cpp)

Demonstrates:

• Loading a de Bruijn graph from disk
• Loading annotations
• Querying sequences against the annotated graph
• Retrieving and displaying matching labels

Test Data (data/)

Pre-built graphs and query sequences for both DNA and Protein alphabets:

• graphs/test_DNA_graph.dbg - Sample DNA de Bruijn graph
• graphs/test_DNA_graph.column.annodbg - Annotations for DNA graph
• test_DNA_query.fa - Query sequences
• Similar files for Protein alphabet

License

This project follows the same license as MetaGraph. See LICENSE for details.