.. _AIRR_Introduction:

AIRR Community 
==============

The Adaptive Immune Receptor Repertoire (AIRR) Community of The Antibody Society is a
research-driven group that is organizing and coordinating stakeholders in the use of
next-generation sequencing (NGS) technologies to study antibody/B-cell and T-cell receptor
repertoires. Recent advances in sequencing technology have made it possible to sample the
immune repertoire in exquisite detail. AIRR sequencing has enormous promise for understanding
the dynamics of the immune repertoire in vaccinology, infectious disease, autoimmunity, and
cancer biology, but also poses substantial challenges. The AIRR Community was established
to meet these challenges.

Introduction to the AIRR Standards
----------------------------------

The AIRR Community is developing a set of standards for describing, reporting,
storing, and sharing adaptive immune receptor repertoire (AIRR) data, such as
sequences of antibodies and T cell receptors (TCRs). Some specific efforts
include:

+ The MiAIRR standard for study reporting that describes minimal information
  about AIRR datasets, including sample collection and data processing information.
+ Data representation and file format specifications for storing large amounts of
  annotated AIRR data.
+ API to query and download AIRR data from repositories/databases as part of the
  AIRR Data Commons.
+ A community standard for software tools which will allow conforming tools to
  gain community recognition.
+ Set of reference software tools for reading, writing and validating data in
  the AIRR standards.
+ A database and web submission frontend for inferred germline genes.

Table of Contents
----------------------------------

.. toctree::
    :maxdepth: 2

    Getting Started <overview>
    Study Reporting (MiAIRR) <miairr/introduction_miairr>
    Data Standards <datarep/overview>
    Data Submission & Query <adc/data_submission>
    Software Libraries <packages/software>
    Data Commons API <api/adc_api_overview>
    Software Compliance Guidelines <swtools/airr_swtools_standard>
    Ontologies and Vocabularies <ontovoc/introduction_ontovoc>
    Reference Germline Database <ogrdb/ogrdb>
    Community <resources/community>
    Glossary <appendix/terms>
    References <appendix/references>