immcantation /

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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. Beginning from raw reads, Python and R packages are provided for pre-processing, population structure determination, and repertoire analysis.


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

Folder Contents
docker Dockerfiles for images hosted on Docker Hub.
docs Sphinx build files for docs hosted on ReadTheDocs.
pipelines Pipeline template scripts for the docker images.
protocols Primer sequences and amplicon designs for published experimental protocols.
scripts Accessory scripts for IMGT, IgBLAST and VDJTools.

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 template pipeline scripts. The image is available on docker hub at kleinstein/immcantation

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 (unstabled) builds.


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