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

In case of questions or requests to extend certain sections of this manual (source), please do not hesitate to open an issue on GitHub or propose your changes via pull requests.

• Installation
  • Install with conda
  • Docker container
  • Install from source
    • Prerequisites
    • Compiling
    • Build configurations
  • Install API
• Quick start
  • Supported alphabets
  • 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
  • Memory mapping
• 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
• Sequence assembly
  • Basic assembly
  • Differential assembly
    • Differential assembly parameters
• Frequently Asked Questions
  • General
    • What is MetaGraph?
    • When should I use MetaGraph?
  • Installation
    • Which installation method?
    • Which alphabet?
  • Graph Construction
    • What k-mer size?
    • How many threads to use?
    • What buffer size?
    • Canonical vs Primary graph?
    • How to handle large datasets?
  • Annotation
    • Which annotation type?
    • How to annotate with counts?
  • Querying
    • How to query?
    • What is discovery_fraction?
    • How to align?
  • Performance
    • Memory requirements?
    • How to speed up construction?
    • How to reduce size?
    • How to reduce RAM usage while querying?
  • Troubleshooting
    • Installation fails
    • Out of memory
    • RowDiff transform generates no output
• Troubleshooting
  • Installation
  • Memory Issues
    • Out of memory
    • Memory cap ignored
  • Annotation Issues
    • Missing k-mer counts file
    • Annotation fails
  • Transform Errors
    • RowDiff transform fails
    • BRWT out-of-memory
    • Missing transform output
  • Alignment Issues
    • Empty sequence error
    • Reverse complement fails
  • API Issues
    • Python API Connection Fails
    • API not installed
  • Docker
  • Performance Tips
    • Speed up construction
    • Reduce Index Size
  • Getting Help
• Resources
  • Preconstructed Indexes
  • MetaGraph Online
  • Contact & Support