Table 2.
Annotation and integrated bioinformatic tools for Lymphocyte Repertoire Data Analysis.
| Bioinformatic tools | Models | Key feature | Limitation | Cases of infection study | Reference |
|---|---|---|---|---|---|
| For VDJ gene assignment | |||||
| IMGT/HighV-QUEST | – | Designed for NGS data; most commonly used | Online version; results sent to user after 1–2 weeks | MERS-CoV (63), influenza (64) | (65) |
| iHMMune-Align | Hidden Markov model (HMM) | Most probable gene segment; accurate IGHD gene identification | Nucleotide insertions or deletions at the gene junctions but not within germline genes | Influenza vaccine (66); EBV, CMV (67) | (48) |
| SoDA2 | Hidden Markov model (HMM) | Probability model; ≥1 probable rearrangement candidates | – | HIV (68) | (50) |
| IgBlast | BLAST algorithm | Open source; gene databases search simultaneously | Relatively low throughput (<1000 per batch) | Dengue virus (69); HIV (70) | (47) |
| Decombinator | Aho–Corasick algorithm | Increased speed | Better matches between query sequence and target sequence needed; only for TCR | M. tuberculosis (71) HIV (72) | (49) |
| Integrated toolkits | |||||
| O-Change | Integrated | Functions unique to BCR analysis (somatic hypermutation analysis, quantifying selection pressure, and calculating sequence chemical properties) | – | West Nile Virus (73) | (54) |
| LymAnalyzer | Integrated | Accurate and complete assignment; polymorphism and SHM analysis | – | – | (56) |
| tcR | Integrated | Based on R; diversity calculation; repertoire comparison; visualization | For output of MiTCR | – | (57) |
| iMonitor | Integrated | Re-alignment to improve accuracy; visualization; PCR and sequencing errors correction | No polymorphism and SHM analysis | – | (59) |
| MiTCR | Integrated | Accurate and higher speed; PCR and sequencing errors correction; sequence quality filter; low quality sequencing data rescue | Strongly related to sequencing quality; only for TCR | CMV (74) | (58) |
| ImmunExplorer (IMEX) | Integrated | Simple statistical analysis and visualization; repertoire comparison | For IMGT/HighV-QUEST outputs | – | (55) |
| VDJtools | Integrated | Diversity assessment, clustering analysis, CDR3 region analysis, and data visualization; simple and user-friendly | Only for TCR; compatible annotation tools needed | – | (61) |
| sciReptor | Integrated | Single-cell sequencing data and HTS data; supports flow cytometry index data; clustering and SHM analysis | – | – | (60) |
| Others | |||||
| Tool for Ig genotype elucidation via Rep-Seq (TIgGER) | Novel V alleles identification; personalized germline database construction | Complementary tools for IMGT; only for novel alleles not distantly related; only for TCR | (75) | ||