Table 2 Bioinformatics tools of immune cell repertoire analysis

Bulk cell repertoire analysis tools

 IGMT/V-QUEST

Analyze cell repertoire generated from rearrangement of nucleotide sequences of antigen receptors (immunoglobulin or antibody, and T cell receptors (TCRs))

[281]

 IgBLAST

Perform sequence analysis of immunoglobulin’s variable domain

[280]

 iHMMune-align

Hidden Markov model-based immunoglobulin heavy chain (IGH) gene characterization program that identifies germline genes in rearranged immunoglobulin sequences

[282]

 MIGEC

Corrects PCR and sequencing errors from immune cell repertoires while maintaining the indigenous diversity

[322]

 MiXCR

Quantitate clonotypes from large immunome sequencing data, identifies germline hypermutations, and corrects PCR/sequencing errors using heuristic multilayer clustering

[283]

 TRUST

Detect tumor-infiltrating T cells by de novo assembly of hypervariable CDR3 sequences, and aligning it to sequence of reference genes from International Immunogenetics Information System (IGMT)

[323]

 GLIPH

Estimates T-cell response diversity by grouping different TCRs sequences that can identify the same antigen-MHC complex

[285]

Single cell repertoire analysis tools

 TraCer

T-lymphocytes single cell RNA sequencing data is used to regenerate paired and full-length TCR sequences

Transcriptional profiles based clonal relationships is used to link T-cell specificity with functional response

[287]

 scTCR-seq

Using single cell TCR sequencing data, accurate identification and assembly of full-length T-cell receptor sequences

[324]

 TRAPes

Algorithm uses paired end, short reads from single cell RNA-seq libraries to reconstruct TCR repertoire, and understand cell state heterogeneity

[325]

 VDJPuzzle

Single cell RNA seq reads overlapping to VDJ or constant region of reference set are assembled using Trinity, filters with IgBlast to create new TCR reference set, and aligns against this new reference

[326]