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pVACseq is a cancer immunotherapy pipeline for the identification of personalized Variant Antigens by Cancer Sequencing (pVACseq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). It enables cancer immunotherapy research by using massively parallel sequence data to predicting tumor-specific mutant peptides (neoantigens) that can elicit anti-tumor T cell immunity. It is being used in studies of checkpoint therapy response and to identify targets for personalized cancer vaccines and adoptive T cell therapies. For more general information, see the manuscript published in Genome Medicine.