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.
IMPORTANT! Immcantation has moved to https://github.com/immcantation/immcantation
To update Git configuration settings use:
git config user.email "your-gh-user@email.com"
git config user.name "your-gh-user-name"
git remote set-url origin git@github.com:immcantation/immcantation.git
This repository contains common documentation, accessory scripts, example 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 | Example pipeline scripts for the docker images. |
| protocols | Primer sequences and amplicon designs for published experimental protocols. |
| scripts | Accessory scripts for IMGT, IgBLAST and VDJTools. |
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>.
Complete usage documentation, API documentation, and several tutorials for the Immcantation framework tools can be found on the Immcantation Portal.