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.

presto-img

pRESTO

  • Quality control
  • Read assembly
  • UMI processing
  • Error profiling
changeo-img

Change-O

  • V(D)J reference alignment standardization
  • Clonal clustering
  • Germline reconstruction
  • Conversion and annotation
alakazam-img

Alakazam

  • Clonal lineage reconstruction
  • Lineage topology analysis
  • Repertoire diversity
  • V(D)J gene usage
  • Physicochemical property analysis
shazam-img

SHazaM

  • Mutation profiling
  • Selection pressure quantification
  • Empirical SHM models
  • Chimera detection
  • Clonal clustering threshold tuning
tigger-img

TIgGER

  • Novel polymorphism detection
  • Genotyping
rdi-img

RDI

  • Repertoire Dissimilarity Index
scoper-img

SCOPer

  • Spectral clonal clustering methods
prestoR-img

prestoR

  • pRESTO report generation