immcantation/base repository overview

⁠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 provides 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

IMPORTANT! Immcantation has moved to https://github.com/immcantation/immcantation⁠

To update Git configuration settings use:

   git config user.email "[email protected]"
   git config user.name "your-gh-user-name"
   git remote set-url origin [email protected]:immcantation/immcantation.git

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.