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ImmuneDB travisci docs codecov pypi docker

ImmuneDB is a database-backed system to analyze and store large amounts (terabytes) of high-throughput B-cell receptor (BCR) and T-cell receptor (TCR) data. Although it can be used as a stand-alone package for comprehensive repertoire profiling, ImmuneDB excels at acting as a central data store and interface between other tools such as IgBLAST, the Immcantation Framework, MiXCR, and VDJtools via AIRR compliant importing and exporting routines.

Feature Highlights

  • Relational storage of repertoire data: Sequences, annotations, clones, lineages, and statistics are all stored in a relational database to promote consistent formatting and easy querying.
  • Consolidated metadata: Custom study, experiment, and replicate metadata is stored alongside your sequencing data in a non-redundant format to avoid inconsistencies and errors over the life of your study.
  • Web interface: ImmuneDB provides a built-in web interface for interactive exploration of data.
  • Interoperability: With AIRR compliant input and output methods, ImmuneDB can interface with other software in the AIRR ecosystem. Other output formats include Change-O and VDJtools.
  • Proven reliability: ImmuneDB is used by multiple labs to manage terabytes of data comprised of billions of sequences in dozens of projects.

Quick Start

To get started immediately, please see the :doc:`Docker installation instructions <install_docker>`.

.. toctree::
    :maxdepth: 2
    :hidden:
    :caption: Getting Started

    Introduction <self>

    install_docker
    install_local

.. toctree::
    :maxdepth: 2
    :hidden:
    :caption: Running the Pipeline

    pipeline_example
    pipeline_full
    modifying
    background

.. toctree::
    :maxdepth: 2
    :hidden:
    :caption: Using a Database

    exporting
    querying
    api

.. toctree::
    :maxdepth: 2
    :hidden:
    :caption: Other

    referencing
    related
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