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snakemake-workflows / dna-seq-neoantigen-prediction

Snakemake workflow for neoantigen prediction
MIT License
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HLA allele callers / HLA typing tools #5

Open dlaehnemann opened 5 years ago

dlaehnemann commented 5 years ago

The recent [review "Alternative Tumour-Specific Antigens][1] lists a number of tools:

tool name repo LICENSE last commits (2019-07-19)
POLYSOLVER https://hub.docker.com/r/sachet/polysolver/ ?? ??
OptiType https://github.com/FRED-2/OptiType) BSD 3-Clause 2019-03-29
PHLAT https://sites.google.com/site/phlatfortype/download "proprietary license" ??
HLAScan www.genomekorea.com/display/tools/HLA_SCAN ?? ??
HLAProfiler https://github.com/ExpressionAnalysis/HLAProfiler "NON-COMMERCIAL USE" 2017-07

Some more could be mined from this list: https://www.cd-genomics.com/an-overview-of-hla-typing.html

Also, are there any benchmarks of these tools?

[1]: Smith, Christof C., Sara R. Selitsky, Shengjie Chai, Paul M. Armistead, Benjamin G. Vincent, and Jonathan S. Serody. 2019. “Alternative Tumour-Specific Antigens.” Nature Reviews Cancer, July, 1. https://doi.org/10.1038/s41568-019-0162-4.