Difference between revisions of "Applications"
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| It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons. | | It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons. | ||
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| + | | [[applications/Transrate|Transrate]] | ||
| + | | Transrate is software for de-novo transcriptome assembly quality analysis | ||
| + | |- | ||
| [[applications/Trinityrnaseq|Trinityrnaseq]] | | [[applications/Trinityrnaseq|Trinityrnaseq]] | ||
| Trinity assembles transcript sequences from Illumina RNA-Seq data. | | Trinity assembles transcript sequences from Illumina RNA-Seq data. | ||
Revision as of 13:35, 19 April 2017
Application Support
Click on the links below for support on the individual and library packages:
- Jump to Libraries or Test Modules
| Package | Description |
| ABySS | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. |
| Anaconda | Anaconda is the leading open data science platform powered by Python. |
| Ansys | ANSYS Fluent software includes broad physical modelling capabilities to model flow, turbulence, heat transfer, and reactions for industrial applications. |
| Avizo | Avizo data visualisation and analysis tool |
| Beast | BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. |
| Bowtie1 | The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences. |
| Bowtie2 | Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method. |
| CMake | CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method. |
| COMSOL | COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems |
| CP2K | CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. |
| Crop | CROP is an unsupervised nucleic acid sequence clustering algorithm. |
| CUDA | CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes. |
| Cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
| Delft3D | Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments. |
| Discovardenovo | DISCOVAR de novo can generate de novo assemblies for both large and small genomes. |
| FDS-SMV | Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations. |
| Ffmpeg | ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source. |
| Flex | Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs which recognize lexical patterns in text. |
| FreeIPMI | FreeIPMI provides in-band and out-of-band IPMI software based on the IPMI v1.5/2.0 specification. |
| Fiji | Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community. |
| Gcc | gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more. |
| GNUplot | Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. |
| Hwloc | hwloc provides command line tools and a C API to obtain the hierarchical map of key computing elements |
| Java | Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented. |
| HPL | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers as well as freely available implementation of the High Performance Computing Linpack Benchmark. |
| IDL | IDL, short for Interactive Data Language, is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging. |
| Intel Parallel Studio | Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing. |
| Libwid | Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers. |
| LS-DYNA | General-purpose finite element program capable of simulating complex real world problems. |
| Maker | MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. |
| Matlab | Numerical Computing Environment. |
| Mercurial | Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independent of network access or a central server. Committing, branching and merging are fast and cheap. |
| Mpich | MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. |
| Mono | .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime. |
| MrBayes | MrBayes: Bayesian Inference of Phylogeny |
| Munge | It is an authentication service that creates and validates user credentials. |
| Mvapich2 | MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance. |
| Ncbi blast | It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. |
| Ncurses | ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner. |
| Netloc | Netloc software package provides network topology discovery tools, and an abstract representation of those networks topologies for a range of network types and configurations. |
| NgSpice | Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. |
| Nwchem | NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems. |
| Open64 | Open64 is a discontinued, free, open source, optimizing compiler for the Itanium and x86-64 microprocessor architectures. |
| Obitools | The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information. |
| Openfoam | OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. |
| OpenMPI | Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes. |
| Orca | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. |
| Paraview | ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. |
| Petsc | PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modelled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism. |
| Perl | Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages. |
| Planatus | Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. |
| Python | Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython. |
| Readline | GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash. |
| Rsem | RSEM is an RNA-Seq transcript quantification program. |
| Samtools | Tools (written in C using htslib) for manipulating next-generation sequencing data |
| SAS | Statistical Analysis System. |
| Scalapack | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers |
| Siesta | SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. |
| SSW | Integrated software libraries, data bases, and system utilities which provide a common programming and data analysis environment for Solar Physics |
| Star-ccm+ | Computational Fluid Package. |
| Stata | Stata is a commercial statistical package, which provides a complete solution for data analysis, data management, and graphics. |
| Tophat | It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons. |
| Transrate | Transrate is software for de-novo transcriptome assembly quality analysis |
| Trinityrnaseq | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
| Utilities | General utilities module including zip, wget and git utilities. |
| Voxfe | VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in biomechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualized easily. |
| Yt | yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically-meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography. |
Libraries
| Library | Description |
| Boost | C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. |
| Cfitsio | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS. |
| Expat | Expat XML parser library in C |
| Fftw3 | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT). |
| Jemalloc | jemalloc is a general purpose malloc implementation that emphasizes fragmentation avoidance and scalable concurrency support. |
| Libgd | The module LibGD is an open source code library for the dynamic creation of images. |
| Libjpeg-turbo | The module Libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression |
| Libpng | The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files. |
| Netcdf-c | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
| Qt | Qt is a cross-platform framework, that is usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper. |
| Zlib | zlib is a software library used for data compression. |
Test Modules
| Library | Description |
| Test-Modules | Access to modules currently in development |
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