ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data

Front Immunol. 2018 Sep 21;9:2107. doi: 10.3389/fimmu.2018.02107. eCollection 2018.


ImmuneDB is a system for storing and analyzing high-throughput immune receptor sequencing data. Unlike most existing tools, which utilize flat-files, ImmuneDB stores data in a well-structured MySQL database, enabling efficient data queries. It can take raw sequencing data as input and annotate receptor gene usage, infer clonotypes, aggregate results, and run common downstream analyses such as calculating selection pressure and constructing clonal lineages. Alternatively, pre-annotated data can be imported and analyzed data can be exported in a variety of common Adaptive Immune Receptor Repertoire (AIRR) file formats. To validate ImmuneDB, we compare its results to those of another pipeline, MiXCR. We show that the biological conclusions drawn would be similar with either tool, while ImmuneDB provides the additional benefits of integrating other common tools and storing data in a database. ImmuneDB is freely available on GitHub at, on PyPi at, and a Docker container is provided at Full documentation is available at

Keywords: B-cell receptor; antibody repertoire analysis; bioinformatics; database; next-generation sequencing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Databases, Nucleic Acid*
  • Humans
  • Receptors, Immunologic / genetics*
  • Sequence Analysis, DNA*
  • Software*


  • Receptors, Immunologic