QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline.
The PacBio Single Molecule Real Time (SMRT) analysis portal is an easy-to-use web-based platform for analyzing 3rd generation sequencing data generated from the PacBio SMRT platform. Currently, workflows for microbial whole genome assembly, resequencing analysis, transcriptome analysis and various data processing steps are available through the portal. For more information on the analysis portal itself, see http://www.pacb.com/devnet/ and the tutorial
CUDA, (the Compute Unified Device Architecture), is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives program developers direct access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
The Intel MPI libraries allow for high performance MPI message passing between processes. They are part of the Intel Cluster Studio package, and are available on MSI systems.
The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. BLAST can compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as translate nucleotide queries or databases in all six frames and compare to protein databases or queries. BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications.
Trinity is a program for the efficient and robust de novo (no reference genome required) reconstruction of transcriptomes from RNA-seq data.
Python is a high level programming language that aims to combine remarkable power with very clear syntax. The Enthought Python Distribution is a cross-platform environment for scientific computing in Python, and includes the Canopy IDE and package manager. MSI has installed an academic-licensed version that includes hundreds of modules, including tools that enable efficient parallel computations.
Cytoscape is an open source bioinformatics software platform for visualizing complex networks and integrating with gene expression profiles and other state data.
Allinea MAPis a profiler for serial and parallel applications written in C, C++, FORTRAN 77, Fortran 90. It supports multiple parallel programming paradigms including MPI, and OpenMP.