HyPhy stands for hypothesis testing using phylogenies. It is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It also features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.
From the man pages:
GeneTorrent is a suite of file transfer applications designed for the optimal transfer of genomic data across computer networks.
You must apply for access to the data following the steps here. MSI is not involved in any way with granting access to the genomic data: direct all enquiries to owners of the CGHub.
Trimmomatic: A flexible read trimming tool for Illumina NGS data. Performs quality filtering, adapter removal, and cropping. Consider using the risstrim.pl script in the riss_util module, which provides a simplified interface for running Trimmomatic.
QUAST stands for QUality ASsesment
RStudio provides open source and enterprise-ready professional software for the R statistical computing environment. RStudio is an IDE for the R programming language.
lumpy is a general probabilistic framework for structural variant discovery.