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. 2023 Apr 17;11:41. doi: 10.1186/s40364-023-00478-5

Table 1.

Common platforms and algorithms for neoantigen prediction

Tools Name Function Tool type Ref
Burrows-Wheeler Alignment tool (BWA) Alignment tool for mutation identification software [34]
ANNOVAR Mutation identification and functional annotation software [35]
MuTect,SomaticSniper Mutation calling and screening software [36, 37]
VarScan Mutations and copy number alterations calling software [38]
FusionCatcher Fusion gene mutation identification software http://code.google.com/p/fusioncatcher/
NetMHCpan/NetMHCpanII, MHCflurry MHC-I/II binding affinity prediction software [41, 4850]
MixMHCpred score, HLAthena MHC-I binding ligands prediction algorithm [42, 51]
MHCnuggets MHC-I or MHC-II binding ligands prediction software [43]
ProGeo-Neo Mutation calling, MHC-I and MHC-II binding affinity and binding ligands prediction software [44]
Differential agretopic index(DAI) Difference identification between mutant and wild sequences algorithm [39]
NetCTLpan T cell epitope and MHC-I binding ligands prediction software [52]
TCRMatch T cell epitope prediction software [46]
PyClone Clonal population prediction algorithm [53]
MuPeXI Neoantigen Immunogenicity identification software [54]
Immune Epitope Database (IEDB) Epitope data database [45]
Tumor Neoantigen Selection Alliance(TESLA) Epitope and sequencing data database [47]