DriverFinder

HccDriverFinder searches through Next Generation Sequencing data for potential mutations or integration events that could drive liver cancer. Features have been added for to identify dominant genotypes, create "circular" genotypes, and combine SAM files. Work has since been published in the American Association for Cancer Research 2018 Journal. Initially created with Amy Lu at Carnegie Mellon University.

Windows environment
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The user may run the application from the source code or the pre-built executable code. The steps below show how to install and run DriverFinder from the pre-built executable code.

Installation:
1. Download all 3 files (DriverFinder_5.2_zip.exe, DriverFinder_5.2_zip.7z.001, & DriverFinder_5.2_zip.7z.002) under the 'DriverFinder_exe' folder.
2. Run the 'DriverFinder_5.2_zip.exe' code to install the application. During the installation, the system will ask the user to provide a folder for the application to be installed.

Execution:
run the 'DriverFinder.exe' code under the folder where the application is installed.


Windows or Mac environment
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1. Make sure that Python 3.x is installed.
2. Download DriverFinder_src folder for the source code and required files.
3. Run the DriverFinder top level code 'DriverFinder_5.2.py'.

DriverFinder screenshot

ChimericSeq_del

Original code from https://github.com/JBSScience/ChimericSeq. Small modifications in order to identify large deletions in the genome.

Windows environment
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The user may run the application from the source code or the pre-built executable code. The steps below show how to install and run ChimericSeq_del from the pre-built executable code.

Installation:
1. Download all 7 files (ChimericSeq_del_v2_zip.exe, ChimericSeq_del_v2_zip.7z.001, ChimericSeq_del_v2_zip.7z.002, ChimericSeq_del_v2_zip.7z.003, ChimericSeq_del_v2_zip.7z.004, ChimericSeq_del_v2_zip.7z.005, ChimericSeq_del_v2_zip.7z.006) under the 'ChimericSeq_del_exe' folder.
2. Run the 'ChimericSeq_del_v2_zip.exe' code to install the application. During the installation, the system will ask the user to provide a folder for the application to be installed in.

Execution:
run the 'ChimericSeq_del.exe' code under the folder where the application is installed.

Windows or Mac environment
===============================
1. Make sure that Python 3.x is installed.
2. Download source code 'ChimericSeq_del_v2.py'.
3. Run 'ChimericSeq_del_v2.py' code.

ChimericSeq_del screenshot


The user guide for the original ChimericSeq can be found at http://www.jbs-science.com/ChimericSeq.php.

To use ChimericSeq_del to identify large deletion, the user needs to use viral reference for both "Host" & "Viral" references and set Configuration "Disable H/V Overlap Alignment" to be True.