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 the AIRR Community (AIRR-C).

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

Core Packages

Click on the images below for more details.

	pRESTO Quality control Read assembly UMI processing Error profiling
	Change-O V(D)J reference alignment standardization Clonal clustering Germline reconstruction Conversion and annotation
	Alakazam Clonal lineage reconstruction Lineage topology analysis Repertoire diversity V(D)J gene usage Physicochemical property analysis
	SHazaM Mutation profiling Selection pressure quantification Empirical SHM models Chimera detection Clonal clustering threshold tuning
	TIgGER Novel polymorphism detection Genotyping
	SCOPer Spectral clonal clustering methods
	prestoR pRESTO report generation
	dowser Phylogenetic analysis on B cell receptor repertoires

Contributed Packages

Click on the images below for more details.

	RDI Repertoire Dissimilarity Index
	RAbHIT Determination of V-D-J haplotypes
	IgPhyML Clonal lineage tree construction Mutation/selection hypothesis testing
	sumrep Generate repertoire summary statistics. Visualize and comparing repertoire summaries.