Immcantation

Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell receptor (BCR) and T cell receptor (TCR) repertoires. The high germline and somatic diversity of the adaptive immune receptor repertoire (AIRR) presents challenges for biologically meaningful analysis - requiring the development of specialized computational methods.

The Immcantation framework provide a start-to-finish analytical ecosystem for high-throughput AIRR-seq datasets. Although Immcantation is focused on BCRs, methods are applicable to TCRs. Beginning from raw reads, Python and R packages are provided for pre-processing, population structure determination, and repertoire analysis.

Repository

This repository contains common documentation, accessory scripts, example pipelines, and docker build files for tools in the Immcantation framework.

Docker Container

We have provided a complete installation of the Immcantation framework, its dependencies, accessory scripts, and IgBLAST in a Docker⁠ image. The image also includes both the IgBLAST and IMGT reference germline sets, as well as several example pipeline scripts. The image is available on Docker Hub at immcantation/suite

Images are versioned through tags with images containing official releases denoted by meta-version numbers (eg, 1.0.0). The devel tag denotes the latest development (unstable) builds. The tag latest is not available. Images can be obtained with the command docker pull immcantation/suite:<tag>.

Documentation

Complete usage documentation, API documentation, and several tutorials for the Immcantation framework tools can be found on the Immcantation Portal⁠.