ASNEO: identification of Alternative Splicing NEOantigens

Introduction

ASNEO is a computational pipeline to identify personalized tumor neoantigens derived from alternative splicing.

Requirement

software

• python3
• bedtools
• pepmatch_db_x86_64 (a script in MuPeXI)
• netMHCpan
• netCTLpan

  The software are packed in src/software.tar.gz

python package

• pandas
• sj2psi
• pysam
• biopython
• sklearn
• xgboost

Usage

input

1. Reference genome file: hg19.fa or GRCh37.fa
2. STAR mapped file: SJ.out.tab and indexed bam(optional)

example

1. git clone https://github.com/bm2-lab/ASNEO.git
2. cd ASNEO/src && tar -xzvf software.tar.gz
3. cd ../test && bash run_ASNEO.sh hg19.fa

   hg19.fa should change to your own reference genome file (must be hg19 or GRCh37)

For detailed usage information, please refer to the ASNEO User Manual

Citation

ASNEO: identification of personalized Alternative Splicing based NEOantigens with RNA-seq, submitted, 2020

Contact

zhangzb@tongji.edu.cn or qiliu@tongji.edu.cn

Tongji University, Shanghai, China