Jin - 2014-05-30

Introduction

INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on Burrow-Wheeler transform.

Software requirements

INTEGRATE is a standalone tool with minimal software dependencies and additional requirements. We hope that users will find it easy to install and use.

samtools

INTEGRATE calls interfaces of samtools (http://samtools.sourceforge.net/) to manipulate BAM files.

libdivsufsort

INTEGRATE calls interfaces of libdivsufsort (https://code.google.com/p/libdivsufsort/) to build Burrow-Wheeler transforms for reference sequences.

CMake

To compile INTEGRATE, CMake (http://www.cmake.org/) is needed. If you don't have CMake in your system, please contact your system administrator to install it.

Note:samtools and libdivsufsort are already included in the source code (INTEGRATE_X_X.tar.gz). You don't need to download them yourself.

Installing

Download and Extract

(1) INTEGRATE_X_X.tar.gz can be downloaded at https://sourceforge.net/projects/integrate-fusion/files/
(2) Extract
tar xvzf INTEGRATE_X_X.tar.gz

Compile INTEGRATE

(1)cd INTEGRATE_X_X
(2)mkdir INTEGRATE-build
(3)cd INTEGRATE-build
(4)cmake ../Integrate/ -DCMAKE_BUILD_TYPE=release
(5)make

now the executable Integrate is at ./bin/

 

Last edit: Jin 2014-05-31