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, 48–50] |
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] |