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.
conda install msisensor-pro
( 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.
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For Debian or Ubuntu:
sudo apt-get install zlib1g-dev libncurses5-dev libncursesw5-dev -
For Fedora, CentOS or RHEL
sudo yum install zlib-devel ncurses-devel ncurses
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colne the repository from our github
git clone https://github.com/xjtu-omics/msisensor-pro -
make
cd msisensor-pro/cpp make -
install
sudo mv msisensor-pro /usr/local/bin/
msisensor-pro <command> [options]
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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 detail in the Files format page
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
If you have any questions, please contact with Peng Jia (pengjia@stu.xjtu.edu.cn) or Kai Ye (kaiye@xjtu.edu.cn).