ImmuneDB is a system to efficiently storage and analyze high-throughput B- and T-cell sequencing data. It provides V- and J-gene identification, clonal assignment, lineage construction, selection pressure calculation, and thorough exporting functionality.
It also provides an intuitive and useful web interface a demo of which you can see here.
To get started immediately, please see the Docker installation instructions.
ImmuneDB is comprised of two GitHub repositories: Python analysis tools (arosenfeld/immunedb) and a web interface (arosenfeld/immunedb-frontend)
The system aims to:
Reduce ad-hoc scripting: Data analysis performed on an ad-hoc basis with custom scripts and data formats is error-prone and leads to inconsistencies. ImmuneDB provides a standardized analysis platform, performing many common tasks automatically.
Minimize flat-files: Flat files are currently the standard method of data exchange in the biological sciences. There are a myriad of drawbacks when using these including a lack of referential integrity, unclear provenance, and non-standardized formats.
ImmuneDB attempts to reduce the need for flat files, through the use of an industry-leading database, MySQL. When data must be exchanged as a flat-file, many export options, including FASTA and tab-delineation, are available.
Interoperate with existing tools: ImmuneDB integrates tools from other researchers to provide features such as lineage construction, genotyping, and selection pressure calculations. Further, ImmuneDB can import and export in a variety of common formats, making it compatible with the larger AIRR ecosystem of tools.