Please click here to see more about MSIsensor-pro in Wiki.
Welcome to try our new software MSIsensor-RNA for MSI detection with RNA-seq data!
If you want to apply the MSIsensor-pro to commercial purposes, please contact Peng Jia (pengjia@stu.xjtu.edu.cn) or Kai Ye (kaiye@xjtu.edu.cn) for a license and get more services.
If you have any questions, please open an issue. If you don't get a prompt response(maybe two working day), please contact with Peng Jia (pengjia@stu.xjtu.edu.cn).
MSIsensor-pro is free for non-commercial use by academic, government, and non-profit/not-for-profit institutions. A commercial version of the software is available and licensed through Xi’an Jiaotong University. For more information, please contact with Peng Jia (pengjia@stu.xjtu.edu.cn) or Kai Ye (kaiye@xjtu.edu.cn).
Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, et al. MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics Proteomics Bioinformatics 2020,18(1). PDF
MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples. For samples of various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in terms of both accuracy and computational cost. If you want to know more detail about MSIsensor-pro, please see the MSIsensor-pro Schematics and Internals page.
MSIsensor-pro evaluates MSI status of a given sample with next generation sequencing (NGS) data. If you have normal-tumor paired DNA sequences, you can use msi (inherited from msisensor) module to score MSI status while pro module would be the option if matched normal is not available.
wget https://github.com/xjtu-omics/msisensor-pro/raw/master/binary/msisensor-pro
chmod +x msisensor-pro
export PATH=`pwd`:$PATH
docker pull pengjia1110/msisensor-pro
docker run pengjia1110/msisensor-pro msisensor-pro
conda install msisensor-pro=v1.2.0
( Recommended For Developers )
Dependent packages including zlib, ncurses and nurses-dev are required for MSIsensor-pro. You may already have these prerequisite packages. If not, you need to run the following code to obtain dependent packages.
-
For Debian or Ubuntu:
sudo apt-get install libbz2-dev zlib1g-dev libcurl4-openssl-dev libncurses5-dev libncursesw5-dev -
For Fedora, CentOS or RHEL
sudo yum install bzip2-devel xz-devel zlib-devel ncurses-devel ncurses
-
colne the repository from our github
git clone https://github.com/xjtu-omics/msisensor-pro -
make
cd msisensor-pro/ ./INSTALL -
install
sudo mv msisensor-pro /usr/local/bin/
msisensor-pro <command> [options]
-
scan
scan the reference genome to get microsatellites information -
baseline
build baseline for tumor only detection -
msi
evaluate MSI using paired tumor-normal sequencing data -
pro
evaluate MSI using single (tumor) sample sequencing data
See more detail in the Key Commands page and Best Practices page.
see details of Input and Output in WiKi.
see details in the Frequently asked questions page in WiKi.
Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, et al. MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics Proteomics Bioinformatics 2020,18(1). PDF
- Peng Jia
- Bowen Liu
- Hao Liang
- Mingzhe Duan