Overview

This chapter introduces the features, operational options, and installation requirements of the data analysis software from Real Time Genomics.

Introduction

RTG software enables the development of fast, efficient software pipelines for deep genomic analysis. RTG is built on innovative search technologies and new algorithms designed for processing high volumes of high-throughput sequencing data from different sequencing technology platforms. The RTG sequence search and alignment functions enable read mapping and protein searches with a unique combination of sensitivity and speed.

The RTG Tools platform provides a subset of the functionality available from the full suite of functions for analyzing and manipulating variant call results. These utilities can be used to perform a variety of tasks such as:

  • Accuracy Evaluation – Compare called variants to a set of known variants to find specificity and sensitivity, check mendelian consistency for the variants from a family, finding basic variant statistics for a set of calls.

  • Result Filtering – Find a subset of variants that match a given set of filtering criteria, extracting only the variant information required for a specific task.

  • Variant Set Manipulation – Merging multiple sets of variant results together, adding additional annotation information to existing variants.

RTG software description

RTG software is delivered as a single executable with multiple commands executed through a command line interface (CLI). Commands are delivered in product packages, and for commercial users each command can be independently enabled through a license key.

Usage:

rtg COMMAND [OPTIONS] <REQUIRED>

See also

For detailed information about RTG command syntax and usage of individual commands, refer to RTG Command Reference.

Installation and deployment

RTG is a self-contained tool that sets minimal expectations on the environment in which it is placed. It comes with the application components it needs to execute completely, yet performance can be enhanced with some simple modifications to the deployment configuration. This section provides guidelines for installing and creating an optimal configuration, starting from a typical recommended system.

RTG software pipeline runs in a wide range of computing environments from dual-core processor laptops to compute clusters with racks of dual processor quad core server nodes. However, internal human genome analysis benchmarks suggest the use of six server nodes of the configuration shown in below.

Table : Recommended system requirements

Processor

Intel Core i7-2600

Memory

48 GB RAM DDR3

Disk

5 TB, 7200 RPM (prefer SAS disk)

RTG Software can be run as a Java JAR file, but platform specific wrapper scripts are supplied to provide improved pipeline ergonomics. Instructions for a quick start installation are provided here.

For further information about setting up per-machine configuration files, please see the README.txt contained in the distribution zip file (a copy is also included in this manual’s appendix).

Quick start instructions

These instructions are intended for an individual to install and operate the RTG software without the need to establish root / administrator privileges.

RTG software is delivered in a compressed zip file, such as: rtg-core-3.3.zip. Unzip this file to begin installation.

Linux and Windows distributions include a Java Virtual Machine (JVM) version 1.8 that has undergone quality assurance testing. RTG may be used on other operating systems for which a JVM version 1.8 or higher is available, such as MacOS X or Solaris, by using the ‘no-jre’ distribution.

RTG for Java is delivered as a Java application accessed via executable wrapper script (rtg on UNIX systems, rtg.bat on Windows) that allows a user to customize initial memory allocation and other configuration options. It is recommended that these wrapper scripts be used rather than directly executing the Java JAR.

Here are platform-specific instructions for RTG deployment.

Linux/MacOS X:

  • Unzip the RTG distribution to the desired location.

  • If your installation requires a license file (rtg-license.txt), copy the license file provided by Real Time Genomics into the RTG distribution directory.

  • In a terminal, cd to the installation directory and test for success

    by entering ./rtg version

  • On MacOS X, depending on your operating system version and configuration regarding unsigned applications, you may encounter the error message:

    -bash: rtg: /usr/bin/env: bad interpreter: Operation not permitted

    If this occurs, you must clear the OS X quarantine attribute with the command:

    $ xattr -d com.apple.quarantine rtg

  • The first time rtg is executed you will be prompted with some questions to customize your installation. Follow the prompts.

  • Enter ./rtg help for a list of rtg commands. Help for any individual command is available using the --help flag, e.g.: ./rtg format --help

  • By default, RTG software scripts establish a memory space of 90% of the available RAM - this is automatically calculated. One may override this limit in the rtg.cfg settings file or on a per-run basis by supplying RTG_MEM as an environment variable or as the first program argument, e.g.: ./rtg RTG_MEM=48g map

  • [OPTIONAL] If you will be running RTG on multiple machines and would like to customize settings on a per-machine basis, copy rtg.cfg to /etc/rtg.cfg, editing per-machine settings appropriately (requires root privileges). An alternative that does not require root privileges is to copy rtg.cfg to rtg.HOSTNAME.cfg, editing per-machine settings appropriately, where HOSTNAME is the short host name output by the command hostname -s

Windows:

  • Unzip the RTG distribution to the desired location.

  • If your installation requires a license, copy the license file provided by Real Time Genomics (rtg-license.txt) into the RTG distribution directory.

  • Test for success by entering rtg version at the command line. The first time RTG is executed you will be prompted with some questions to customize your installation. Follow the prompts.

  • Enter rtg help for a list of rtg commands. Help for any individual command is available using the --help flag, e.g.: ./rtg format --help

  • By default, RTG software scripts establish a memory space of 90% of the available RAM - this is automatically calculated. One may override this limit by setting the RTG_MEM variable in the rtg.bat script or as an environment variable.

License Management

Commercial distributions of RTG products require the presence of a valid license key file for operation.

The license key file must be located in the same directory as the RTG executable. The license enables the execution of a particular command set for the purchased product(s) and features.

A license key allows flexible use of the RTG package on any node or CPU core.

To view the current license features at the command prompt, enter:

$ rtg license

See also

For more data center deployment and instructions for editing scripts, see Administration & Capacity Planning.

Technical assistance and support

For assistance with any technical or conceptual issue that may arise during use of the RTG product, contact Real Time Genomics Technical Support via email at support@realtimegenomics.com

In addition, a discussion group is available at: https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-users

A low-traffic announcements-only group is available at: https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-announce