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AIRR Standards 1.3 documentation

  • Getting Started
    • AIRR Rearrangement TSV Interoperability Example
    • ADC API Query and Analysis Example
    • Scientific Query Scenarios for AIRR Data Commons API
  • Release Notes
  • AIRR Standards
    • Study Reporting (MiAIRR)
      • MiAIRR Data Elements
      • National Center for Biotechnology Information (NCBI) Submission
        • Guide for submission of AIRR-seq data to NCBI
        • MiAIRR-to-NCBI Submission Manual
        • MiAIRR-to-NCBI Specification
      • Requirement levels of fields
      • Metadata annotation guidelines
    • Data Model
      • Requirement levels of fields
      • Repertoire Schema
      • Rearrangement Schema
      • Alignment Schema (Experimental)
      • Clone and Lineage Tree Schema (Experimental)
      • Cell Schema (Experimental)
    • V(D)J Sequence Representation
    • Metadata Representation
    • Software Guidelines
      • Compliance Checklist for AIRR Software Tools
      • List of Compliant Tools
      • Recommended Software Evaluation Data Sets
    • Data Commons API
    • Ontologies and Vocabularies
      • Report Sprint 11/2018
      • Report Sprint 04/2020
    • Schema Release Notes
  • Data Submission and Query
    • MiAIRR to NCBI submission guide
      • Guide for submission of AIRR-seq data to NCBI
      • MiAIRR-to-NCBI Submission Manual
      • MiAIRR-to-NCBI Specification
    • CEDAR's CAIRR submission pipeline
    • VDJServer Community Data Portal
    • iReceptor Turnkey Repository
    • OGRDB
      • The Genbank/ENA Workflow.
    • AIRR Data Commons
  • Software
    • Python Library
      • API Reference
      • Commandline Tools
      • Release Notes
    • R Library
      • Usage Vignette
      • Reference Manual
        • read_airr
        • write_airr
        • validate_airr
        • load_schema
        • Schema-class
        • ExampleData
      • Release Notes
    • ADC API Reference Implementation
    • Applications Supporting the Rearrangement Schema
    • AIRR Data Commons Repositories
  • Community
    • Applications Supporting the Rearrangement Schema
    • AIRR Data Commons Repositories
  • Glossary
  • References
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AIRR Software WG - List of Tools Certified as CompliantΒΆ

The following tools have been certified as compliant with v1.0 of the guidelines:

Software

Version

Support

Reference

SONAR

3

Output

Schramm et al. Front Immunol, 2016.

ImmuneDB

0.29.10

Input

Rosenfeld et al. Front Immunol, 2018,

Scirpy

0.4.2

Input

Sturm et al. Bioinformatics, 2020,

Immcantation Framework

4

Input, Output

Vander Heiden et al. Bioinformatics, 2014,; Gupta et al., Bioinformatics, 2015,

CompAIRR

1.3.1

Input

Rognes T, Scheffer L, Greiff V, Sandve GK 2021 (preprint),

ImmuneML

2.0.4

Input, Output

Pavlovic et al., BioRxiv, 2021 immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires (preprint),

Dandelion

0.1.10

Output

Stephenson et al., Nature Medicine, 2021 Single-cell multi-omics analysis of the immune response in COVID-19,

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AIRR Software WG - Compliance Checklist for AIRR Software Tools

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Evaluation Data Sets

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