Home

General Introduction

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 which required matched normal samples 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.

Scopes of MSIsensor-pro

MSIsensor-pro can evaluate MSI 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. If you only have tumor sample, you can use pro module to do it.

How to install MSIsensor-pro?

Directly using binary version

  wget https://github.com/xjtu-omics/msisensor-pro/raw/master/binary/msisensor-pro
  chmod +x msisensor-pro 
  export PATH=`pwd`:$PATH

Install using bioconda

 conda install msisensor-pro

Install from source code

Install the dependencies

If you want to make MSIsensor-pro by yourself, you need dependent packages including zlib, ncurses and nurses-dev. You may already have these prerequisite packages. If not, you need to run the following code to finish it.

• 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

Build MSIsensor-pro from source code

• colne the repository from our github

  git clone https://github.com/xjtu-omics/msisensor-pro
  

• make

  cd msisensor-pro
  ./INSTALL
  

• install

  sudo mv cpp/msisensor-pro /usr/local/bin/
  

How to use MSI ?

Usage:

  msisensor-pro <command> [options]

Key Commands:

• 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.

Files format

see detail in the Files format page