Immcantation: An Integrated Framework for Adaptive Immune Receptor Repertoire Analysis (original) (raw)

Welcome to the Immcantation Portal

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.

Immcantation supports both the original Change-O standard and the new Adaptive Immune Receptor Repertoire (AIRR) standard developed by theAIRR Community (AIRR-C).

The different tools are available from PyPi, CRAN and GitHub. Versioned containers with all tools installed are hosted on Docker Hub.

Core Packages

Click on the images below for more details.

	Alakazam Repertoire diversity V(D)J gene usage Physicochemical property analysis
	Change-O V(D)J alignment with IgBLAST and IMGT
	Dowser B cell lineage trees Migration and differentiation analysis Detect ongoing evolution over time
	pRESTO Bulk BCR sequence data pre-processing Read assembly and QC UMI processing
	SCOPer Identify clonal relationships
	SHazaM Clonal clustering threshold tuning Mutation profiling Selection pressure quantification Empirical SHM models
	TIgGER Novel polymorphism detection Genotyping

Contributed Packages

Click on the images below for more details.

	IgPhyML Method to build lineage trees Mutation/selection hypothesis testing Best used via Dowser package
	RAbHIT Determination of V-D-J haplotypes
	PIgLET Tools to improve genotype inference
	RDI Repertoire Dissimilarity Index
	sumrep Generate repertoire summary statistics. Visualize and comparing repertoire summaries.