TIminer: NGS data mining pipeline for cancer immunology and immunotherapy.

ABSTRACT

SUMMARY: Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from next-generation sequencing data. TIminer enables integrative immunogenomic analyses, including human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates and quantification of tumor immunogenicity. AVAILABILITY AND IMPLEMENTATION TIminer is freely available at http//icbi.i-med.ac.at/software/timiner/timiner.shtml. CONTACT zlatko.trajanoski@i-med.ac.at. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.