User Manual

Welcome to the user manual of MetaGraph!

This manual includes setup instructions and usage tutorials outlining the key use cases for the MetaGraph framework, a software platform for indexing and analysis of very large sequence collections.

Attention

This documentation is currently under development (source). In case of specific questions or requests to extend certain sections of this manual, please do not hesitate to open an issue on GitHub or propose your changes via a pull request.

• Installation
  • Install with conda
  • Docker container
  • Install from source
    • Prerequisites
    • Compiling
    • Build configurations
  • Install API
• Quick start
  • Construct graph
    • Basics
    • Construct from KMC counters
    • Transform to other representations
    • Transform to sequences
    • Construct canonical graph
    • Construct primary graph
    • Graph cleaning
  • Annotate graph
    • Annotate sequence headers
    • Annotate source filenames
    • Annotate using custom labels
    • Index k-mer counts
    • Index k-mer coordinates
    • Transform annotation
  • Query index
    • Using Command Line Interface
    • Using Python API
  • Column operations
    • Examples
    • Aggregating function
• Snakemake workflows
  • Installation
  • Creating graphs and annotations
    • Usage
    • Workflow management
    • Directly invoking Snakemake workflow
• Python API
  • Installation
  • Sequence search
    • metagraph.client.GraphClient.search()
    • Search with alignment
    • Querying k-mer abundance and coordinates
  • Sequence alignment
    • metagraph.client.GraphClient.align()
  • Examples
    • Example of search in MetaSUB
    • Search multiple graphs in parallel
    • Query a locally hosted index
    • Other examples
• Sequence search
  • Align sequences to the graph
    • Exact k-mer matching
    • Sequence-to-graph alignment
    • Additional parameters
  • Query sequences against the index
    • Parameters for exact k-mer matching
    • Parameters for alignment
• Sequence assembly
  • Basic assembly
  • Differential assembly
    • Differential assembly parameters
• Resources
  • Preconstructed indexes
  • MetaGraph Online