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.

Component Packages

Click on the images below for more details.

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pRESTO

  • Quality control

  • Read assembly

  • UMI processing

  • Error profiling

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Change-O

  • V(D)J reference alignment standardization

  • Clonal clustering

  • Germline reconstruction

  • Conversion and annotation

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Alakazam

  • Clonal lineage reconstruction

  • Lineage topology analysis

  • Repertoire diversity

  • V(D)J gene usage

  • Physicochemical property analysis

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SHazaM

  • Mutation profiling

  • Selection pressure quantification

  • Empirical SHM models

  • Chimera detection

  • Clonal clustering threshold tuning

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TIgGER

  • Novel polymorphism detection

  • Genotyping

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RDI

  • Repertoire Dissimilarity Index

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SCOPer

  • Spectral clonal clustering methods

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prestoR

  • pRESTO report generation

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IgPhyML

  • Clonal lineage tree contruction

  • Mutation/selection hypothesis testing