From: Best practices for bioinformatic characterization of neoantigens for clinical utility
Tool categories | Function and examples |
---|---|
Alignment | DNA: Bwa-mem [161] |
Sequence data QC | Picard (http://broadinstitute.github.io/picard/), FastQC (https://github.com/s-andrews/FastQC), RSeQC [164], MultiQC (https://github.com/ewels/MultiQC) (note that MultiQC supports an extensive list of additional QC tools) |
Variant callers | SNV/Indel: Mutect [19], Strelka [20], VarScan2 [21], SomaticSniper [22], Shimmer [165], VarDict [166], deepSNV [167], EBCall [40] Structural variants: Pindel [43], Manta [168], Lumpy [169] Fusions: STAR-Fusion [48], Pizzly [47], SOAPfuse [170], JAFFA [49], ChimPipe [171], GFusion [50], INTEGRATE [51] |
Variant call format (VCF) manipulation | Vt decompose (https://github.com/atks/vt), GATK (https://github.com/broadinstitute/gatk) (e.g., SelectVariants, CombineVariants, LeftAlignAndTrimVariants) |
Variant annotation | Variant Effect Predictor (VEP) (https://github.com/Ensembl/ensembl-vep) (SNV/Indel), AGFusion [172] (RNA fusions), bam-readcount (https://github.com/genome/bam-readcount), VAtools (https://github.com/griffithlab/VAtools) |
Gene or transcript abundance estimation | |
HLA typing | Class I: Optitype [69], Polysolver [70] Class I and II: Athlates [70, 175], HLAreporter [176], HLAminer [176, 177], HLAscan [72, 178], HLA-VBSeq [72], PHLAT [71], |
Peptide processing | Proteasome cleavage: NetChop20S [89], NetChopCterm [89], ProteaSMM [89, 90], PAProC [179] (Class I), PepCleaveCD4 [91] (Class II) TAP transport efficiency: [90] (no specific tool name) |
MHC binding predictors | Class I predictors: SMM [111], SMMPMBEC [112], Pickpocket [113], NetMHC [114], NetMHCpan [87], NetMHCcons [180], MHCflurry [102], MHCnuggets [181], MHCSeqNet [103], EDGE [104] Class II predictors: SMMAlign [111], NNAlign [182], ProPred [183], NetMHCII(2.3) and NetMHCIIpan(3.2) [116], TEPITOPE [184], TEPITOPEpan [185], RANKPEP [186], MultiRTA [187], OWA-PSSM [188] |
Neoantigen prioritization pipelines | pVACtools [8], Vaxrank [9], MuPeXI [119], TIminer [120], Neoepiscope [189], TSNAD [190], EpiToolKit [123], NeoepitopePred [122], TepiTool (IEDB) [191], ScanNeo [192], CloudNeo [193], NeoPredPipe [118] |
Peptide creation and delivery | |
TCR repertoire profiling | LymAnalyzer [194], MiXCR [147], MIGEC [148], pRESTO [195], TRUST [196], TraCeR [145], VDJtools [197], VDJviz [198], ImmunoSEQ [199], GLIPH [151] |
Immune cell profiling | CIBERSORT [152], TIMER [153], quanTIseq [200], immunophenogram [201], MCPcounter [202], SSGSEA [203] |