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.
|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.|
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,
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.