Geno-DeBasher Package for Genomic Variant Calling

Introduction

Geno-DeBasher is a software package designed to execute bioinformatics pipelines, with a particular focus on cancer genomics and 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 pairs of bam files.
• Automation of bam file downloading from EGA, GDC (including TCGA), ICGC and AWS repositories, or use of bam files already present locally.
• Pipeline processes automating bam file manipulation, filtering and summarization, and the handling of reference genomes.
• Processes implementing single nucleotide, copy number and structural variant calling, with tools such as Manta, Strelka, Delly, Lumpy, Platypus, LoFreq, Facets, ASCAT, Sequenza and CNVkit.
• Processes implementing microsatellite instability (MSI) analysis, with MSIsensor-pro.
• Basic and extended versions of the pipelines, the latter processing each contig of the genome in parallel, for larger inputs.
• Automated installation of the tools that the pipelines use, as Conda environments, through the Conda support of DeBasher.

Distribution Details

Geno-DeBasher has been coded using Bash shell-scripting, Python and R. It runs wherever DeBasher does: it is developed and tested on Linux, and also runs on Windows through WSL2; macOS has not been tested yet (see the installation instructions of DeBasher). 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), version 3.

Installation

Requirements

The pipeline modules provided by Geno-DeBasher are designed to be executed by the DeBasher software package. Therefore, DeBasher and all of its requirements should be installed first, following its installation instructions, which also cover the autotools needed to configure this package and the setup on Linux, Windows (WSL2) and macOS.

Most pipelines also need Conda, from which DeBasher installs the tools that they use, and some of them need further third-party software (see below).

Building and Installing

Once DeBasher is installed, you can proceed with the installation of Geno-DeBasher 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 installation directory of DeBasher (the one that contains its bin/ and lib/debasher/ directories).

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 has installed DeBasher in /home/user1/debasher and 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 --with-debasher=/home/user1/debasher --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. Each of the following options gives the installation directory of an external tool, and is only needed by the processes that use that tool:

• --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.
• --with-decsingle=<DIR> and --with-decsingle-java=<DIR>: allow Geno-DeBasher to use the decsingle tool, and the Java it runs with, to decrypt the files downloaded from EGA.
• --with-platypus=<DIR> and --with-lumpy=<DIR>: use an installation of the Platypus and Lumpy variant callers of your own.

Third Party Software

Conda

Conda is used by DeBasher to install, in environments of their own, the bioinformatics tools that the pipelines of Geno-DeBasher run.

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.

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).
• The technical documentation of DeBasher, which explains how to execute the pipelines and how to write new ones.

If you need additional help, you can:

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