MetaGraph Documentation

Comprehensive user manual for the MetaGraph framework - a software platform for indexing and analysis of very large sequence collections

Version 1.0Open Source

Getting Started

Installation
Get started with conda, Docker, or build from source

Learn how to install MetaGraph using conda, Docker containers, or compile from source with custom build configurations.

View Installation Guide
Quick Start
Learn to construct graphs, annotate, and query indexes

Step-by-step tutorial covering graph construction, annotation, transformation, and querying using both CLI and Python API.

View Quick Start

Core Features

Sequence Search
Align sequences to graphs with exact k-mer matching

Perform exact k-mer matching and sequence-to-graph alignment for efficient sequence search.

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Snakemake Workflows
Automated workflows for graph and annotation creation

Use Snakemake workflows to automate graph construction and annotation processes at scale.

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Sequence Assembly
Basic and differential assembly capabilities

Assemble sequences from graphs with support for differential assembly and custom parameters.

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API & Development

Python API
Programmatic access to sequence search, alignment, and graph operations

Complete Python API documentation including sequence search with alignment, k-mer abundance queries, coordinate indexing, and examples for MetaSUB searches and parallel graph queries.

View API Documentation

Resources

Preconstructed Indexes & MetaGraph Online
Access ready-to-use indexes and online query interface

Explore preconstructed indexes for various datasets and use MetaGraph Online for web-based sequence queries without local installation.

View ResourcesMetaGraph Online

This documentation is currently under development. For questions or requests to extend certain sections, please open an issue on GitHub or propose changes via a pull request.