Immcantation Tutorials

Each tool in the framework has its own documentation site, with detailed usage information and examples. A good starting point to familiarize yourself with the framework is to follow one the tutorials listed here.

Introductory Webinar and Jupyter Notebook

For a detailed use example for each Immcantation tool see the Jupyter notebook from our introductory webinar in the repository. If you don’t want to execute the Jupyter notebook yourself, you can explore a website version of it here. This webinar covers:

• V(D)J gene annotation and novel polymorphism detection

• Inference of B cell clonal relationships

• Diversity analysis

• Mutational load profiling

• Modeling of somatic hypermutation (SHM) targeting

• Quantification of selection pressure

Single-cell Analysis

For information on how to process 10x Genomics data to be analyzed with Immcantation, we offer an introductory tutorial for new users:

• 10x Genomics V(D)J Sequence Analysis Tutorial

Vignettes

Detailed usage documentation and tutorials for each individual tool in Immcantation are provided in the main documentation pages for each tool. The following list of shortcuts cover common analyses. Note, each link will leave the Immcantation portal page.

• Assembling raw reads from simple Illumina sequencing protocols with pRESTO
• Assembling raw reads from 5'RACE UMI barcoded Illumina sequencing protocols with pRESTO
• Processing 10x Genomics Cell Ranger data with Change-O
• Processing IgBLAST data with Change-O
• Processing IMGT/HighV-QUEST data with Change-O
• Building lineage trees with IgPhyML
• Assigning clonal groups with SCOPer
• Basic gene usage analysis with Alakazam
• Clonality and diversity analysis with Alakazam
• Mutational load analysis with SHazaM
• Selection pressure analysis with SHazaM
• Building SHM targeting models with SHazaM
• Novel allele detection and genotyping with TIgGER