Geno-DeBasher Package for Genomic Variant Calling

Introduction

Geno-DeBasher is a software package designed to execute bioinformatics pipelines, with a particular focus on genome variant calling. Pipelines are implemented as modules that can be executed by means of the DeBasher flow-based programming Bash extension. Geno-DeBasher also provides some utilities useful to automate experiments on complete datasets.

The Geno-DeBasher package was created and is currently maintained by Daniel Ortiz-Martínez. Daniel is an experienced machine learning researcher and also holds an MSc degree in Bioinformatics.

Features

The package incorporates the following features:

• Execution of pipelines processing normal-tumor files.
• Automation of bam file downloading.
• Pipeline processes automating bam file manipulation.
• Processes implementing single nucleotide/copy number/structural variant calling.
• Processes implementing microsatellite instability (MSI) analysis.
• Parallel versions of multiple variant calling tools.

Distribution Details

Geno-DeBasher has been coded using shell-scripting. Geno-DeBasher is known to compile on Unix-like and Windows (using Cygwin) systems. See the "Documentation and Support" section of these instructions if you experience problems during compilation.

It is released under the GNU Lesser General Public License (LGPL).

Installation

Basic Installation Procedure

To install Geno-DeBasher, first you need to install the autotools (autoconf, autoconf-archive, automake and libtool packages in Ubuntu). If you are planning to use Geno-DeBasher on a Windows platform, you also need to install the Cygwin environment. Alternatively, the tool can also be installed on Mac OS X systems using MacPorts.

Pipeline modules provided by Geno-DeBasher are designed to be executed by the DeBasher software package. Therefore, DeBasher and all of its requirements should also be installed before installing Geno-DeBasher.

On the other hand, some of the functionality incorporated by Geno-DeBasher requires the previous installation of third-party software (see below).

Once the autotools are available (as well as other required software such as Cygwin or MacPorts), you can proceed with the installation of the tool by following the next sequence of steps:

1. Obtain the package using git:

   $ git clone https://github.com/daormar/geno-debasher.git
   

   Or download it in a zip file

2. cd to the directory containing the package's source code and type ./reconf.

3. Type ./configure --with-debasher=<DIR> to configure the package (where <DIR> is the build directory of the DeBasher package).

4. Type make to compile the package.

5. Type make install to install the programs and any data files and documentation.

6. You can remove the program binaries and object files from the source code directory by typing make clean.

By default the files are installed under the /usr/local/ directory (or similar, depending on the OS you use); however, since Step 5 requires root privileges, another directory can be specified during Step 3 by typing:

 $ configure --with-debasher=<DIR> --prefix=<absolute-installation-path>

For example, if "user1" wants to install the Geno-DeBasher package in the directory /home/user1/geno-debasher, the sequence of commands to execute should be the following:

 $ ./reconf
 $ configure --prefix=/home/user1/geno-debasher
 $ make
 $ make install

The installation directory can be the same directory where the Geno-DeBasher package was decompressed.

Alternative Installation Options

The Geno-DeBasher configure script can be used to modify the toolkit behavior. Here is a list of current installation options:

• --with-icgcscor=<DIR>: allows Geno-DeBasher to use the ICGC score client. The ICGC score client can be used to interact with cloud repositories.
• --with-aspera=<DIR>: enables use of the Aspera commercial file transfer protocol to download bam files.
• --with-egadecrypt=<DIR>: allows Geno-DeBasher to access decryption functionality provided by the EGACryptor client.

Third Party Software

ICGC Score Client

The ICGC score client allows to download content, including bam files from cloud repositories. The client can be downloaded after clicking in this link.

ASPERA Connect

ASPERA Connect is a file transfer protocol that may provide faster transfer speeds with respect to the standard FTP protocol. The ASPERA download client can be used by Geno-DeBasher to download bam files. The client can be downloaded here.

EGA Decryptor

EGACryptor is a JAVA based client providing encryption and decryption functionality. It is used by Geno-DeBasher to decrypt information downloaded from EGA repositories.

Current Status

The Geno-DeBasher package is under development. Basic usage instructions are being added.

Documentation and Support

Project documentation is being developed. Such documentation includes:

• These instructions.
• A set of slides ("slides.pdf" under the "doc" directory).

If you need additional help, you can:

• use the github issue tracker.
• send an e-mail to the author.