Table 1 Overview of evaluated tools for NGS-based HLA genotyping. Checkmarks and crosses indicate which NGS methods (WES and/or RNA-Seq) and input file types (FASTQ and/or BAM) are supported and for which genes predictions can be made. The tools in the upper part of the table are benchmarked in this study. Tools in the lower part of the table did not fulfil our inclusion criteria and were not further considered. * Works preferentially with WGS instead of WES data
From: Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data
Data type | Input filetype | HLA loci | Version | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WES | RNA | BAM | FASTQ | A | B | C | DPA1 | DPB1 | DQA1 | DQB1 | DRB1 | |||
Included | arcasHLA [18] | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 0.2.0 |
HLA-HD [30] | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 1.3.0 | |
HLA-VBSeq [31] | ✓* | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 2 | |
HLA*LA [32] | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 1.0.1 | |
HLAforest [33] | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 1 | |
HLAminer [34] | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 1.4 | |
HLAscan [35] | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 2.1.4 | |
Kourami [36] | ✓* | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 0.9.6 | |
Optitype [16] | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | 1.3.5 | |
PHLAT [37] | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | 1.1 | |
Polysolver [8] | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | 4 | |
seq2HLA [38] | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 2.3 | |
xHLA [39] | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | 0.0.0 | |
Not included | ALPHLARD-NT [40] | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
ATHLATES [41] | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ||
HLAProfiler [42] | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
HLAreporter [43] | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
HLAssign [44] | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
OncoHLA [45] | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
PolyPheMe [46] | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ||
SNP2HLA [47] | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
SOAP-HLA [48] | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||