ppflrs/rtg-core

RTG Core: Software for alignment and analysis of next-gen sequencing data.

RTG Core Non-commercial

Copyright (c) 2014 Real Time Genomics Ltd

This software is provided under the Real Time Genomics Ltd Software Licence Agreement for Academic Non-commercial Research Purposes only. See LICENSE.txt

Introduction

There are many software packages available for next-gen sequencing analysis, here are some of the reasons to use RTG:

• Comprehensive, cohesive, fast, sensitive and accurate variant calling pipeline from FASTQ through to high-quality variants.
• Robust, easy to use, and well supported.
• Fast and accurate alignment, supporting popular sequencing technologies, including alignment of Complete Genomics Inc reads.
• Automatic base-quality recalibration computed on-the-fly during mapping and applied during variant calling.
• Variant calling both simple SNPs and complex haplotypes, automatically realigning when necessary.
• Pedigree-aware pipeline, joint Bayesian calling of multiple samples in pedigrees with varying degrees of relatedness, from unrelated, trios, quads, larger families, multi-generation pedigrees.
• Pedigree-aware joint calling automatically includes de novo discovery, including specific confidence scoring that the variant is de novo. Again, this includes information from larger families where available, not just trios. Offspring variant calls are automatically phased from inheritance.
• Variant calling allows specification of population priors in either from general population variants or those in previously called samples.
• Sex-aware pipeline, automatically mapping to the correct chromosomes for the sex of the sample, performing diploid or haploid variant calling as appropriate (including PAR regions).
• Joint Bayesian somatic variant detection, including support for contamination, and providing post-calling updated contamination estimate. Supports site-specific somatic mutation priors that allow databases such as dbSNP/COSMIC/etc to support the somatic calling.
• Tools for Q/A and sample checking: coverage analysis, detect chromosome abnormalities, sample mislabelling, incorrect pedigree.
• Includes sophisticated variant comparison tools for benchmarking and ROC analysis to guide variant scoring and filtering.
• Fast and comprehensive metagenomic analysis pipelines.
• Species frequency composition and abundance analysis, including bounds estimates and confidence scores both at the species and higher taxon levels.
• Species reported using both tabular data reports and interactive Krona HTML pie charts.
• Contaminant filtering and sample similarity analysis.
• Includes tools for building and managing species reference databases that include taxonomic structure (prebuilt databases are also available).
• Search reads directly against protein databases for functional analysis.
• Reproducible results -- unlike many other tools, the results don't change when you enable multi-threading or when you repeat the same run twice.

RTG Core is available pre-packaged directly from our website, or follow the instructions below to build from this repository.

Support

A PDF user manual is included in the installation or can be viewed online.

You can use the commands in RTG Core to format your own reference datasets, or download common pre-formatted references from our website.

An rtg-users discussion group is now available for general questions, tips, and other discussions.

To be informed of new software releases, subscribe to the low-traffic rtg-announce group.

If you require a license for commercial use or wish to purchase commercial support contact us via [email protected].

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Prerequisites for building from source

• Java 1.7 or later
• apache ant 1.9 or later

Check out source code for both RTG Tools and RTG Core

Building RTG Core requires the source code to both RTG Tools and RTG Core, so you must clone both repositories:

$ git clone https://github.com/RealTimeGenomics/rtg-tools.git
$ git clone https://github.com/RealTimeGenomics/rtg-core.git
$ cd rtg-core

To update, you will need to perform a git pull on both repositories. Advanced users may use git subtree to have both RTG Tools and RTG Core within a single repository (it's what we use during development).

Compile / run unit tests

$ ant runalltests

Building RTG Core package

To build the RTG Core Non-Commercial package which can be locally installed and run:

$ ant zip-nojre

This will create an installation zip file under dist.

Installation

Uncompress the installation zip:

$ cd /my/install/dir/
$ unzip /path/to/rtg-core/dist/rtg-core-VERSION-nojre.zip

Follow the instructions contained in the README.txt. This build will use the system Java by default, so ensure it is Java 1.7 or later.

For a nice demonstration of the features of RTG Core for sex and pedigree aware mapping and variant calling on data generated from scratch using the RTG Core simulation tools, run the demo-family.sh script contained in the scripts of the installation directory:

$ cd /my/install/dir/rtg-core-VERSION/
$ ./scripts/demo-family.sh $PWD/rtg