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
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