bm2lab/ituneos repository overview

Usage:

1. Pull image from dockerhub: docker pull bm2lab/ituneos
2. Run the image in interactive mode with your dataset: docker run -it -v /your/path/to/dataset/:/home/bioworker/dataset bm2lab/ituneos /bin/bash
3. Change directory into /home/bioworker/project/iTuneos: cd /home/bioworker/project/iTuneos
4. Download reference data: bash data_download.sh
5. iTuneos has two modes, WES mode and VCF mode. WES mode accepts WES and RNA-seq sequencing data as input, it conduct sequencing quality control, mutation calling, hla typing, expression profiling, neoantigen prediction, neoantigen filtering and neoantigen annotation. VCF mode accepts mutation VCF file, expression profile, copy number profile and tumor cellularity as input, it performs neoantigen prediction, neoantigen filtering and neoantigen annotation directly on input file. You should first replace the input file path in config_WES.yaml or config_VCF.yaml. Then use these two mode by: python iTuneos.py WES -i config_WES.yaml or python iTuneos.py VCF -i config_VCF.yaml

Other information about iTuneos, please refer to

1. iTunes Github repository (https://github.com/bm2-lab/iTuneos⁠)
2. Citation iTuneos: identification of personalized Tumor neoantigens from next-generation sequencing data, Submitted, 2019.