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.

Click on the relevant section of the image below for more details.

For an overview of AIRR-seq analysis, check out:

Yaari and Kleinstein. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Medicine. 7, 121 (2015). doi:10.1186/s13073-015-0243-2

AIRR-seq analysis tutorial

Slides and data from the tutorial presented by Jason Vander Heiden at the Stochasticity and Control of Immune Repertoires Group Conference (Israel, June 18 - June 23, 2017).

How to Cite

To cite the pRESTO software package in publications please use:

Vander Heiden JA*, Yaari G*, Uduman M, Stern JNH, O’Connor KC, Hafler DA, Vigneault F, Kleinstein SH. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics 30, 1930-2 (2014). doi:10.1093/bioinformatics/btu138

To cite the Change-O, Alakazam, SHazaM and TIgGER software package in publications please use:

Gupta NT*, Vander Heiden JA*, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 31, 3356-8 (2015). doi:10.1093/bioinformatics/btv359

Additional citations for specific methods within Alakazam, SHazaM and TIgGER may be determined using the citation() function witin R.


Jason A. Vander Heiden, Namita T. Gupta, Mohamed Uduman, Daniel Gadala-Maria, Susanna Marquez, Julian Zhou, Rouyi Jiang, Ang Cui, Nima Nouri, Chris R. Bolen, Gur Yaari, Steven H. Kleinstein

Contact Information

If you have questions you can email Steven Kleinstein.

For additional computational immunology software from the Kleinstein Lab see our website.