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

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.
(© The Author(s) 2017. Published by Oxford University Press.)