/category/bioinformatics

  • The Bioconda Environment on Rivanna

     Bioconda Python packages Many bioinformatics Python packages are now maintained and available for the popular Anaconda Python distribution. Python packages for the Anaconda distribution are distributed through a variety of different bundles, called channels. The bioconda channel is specifically set up for the maintenance and distribution of popular bioinformatics packages. On Rivanna, we offer two bioconda modules, one using Python 2.7 and the other using Python 3.6. Available Versions The current installation of Bioconda incorporates the most popular packages. To find the available versions and learn how to load them, run: module spider bioconda The output of the command shows the available Bioconda module versions.
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     HPC, software, bioinformatics    

  • Bioinformatics on Rivanna

     Overview Many commonly used bioinformatics software packages on Rivanna are available as individual modules or as Python packages bundled in the bioconda modules. Please see our HowTo for more information about using this software on Rivanna. Software Availability If a particular package is not available, several options are available. If it is sufficiently widely used, Research Computing staff will install it as a new module. If we determine that it is too specialized, you can install it yourself. Please use permanent storage such as your home directory to install software. If you have difficulty we can assist you to install the package.
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     HPC, software, bioinformatics    

  • Nvidia Clara Parabricks

     Overview Nvidia Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data. It contains GPU-enabled versions of popular bioinformatics tools such as the aligners BWA-Mem and STAR. Loading the container On Rivanna, Clara Parabricks is available as a Singularity container. To load the clara-parabricks container module, you can type: module load singularity clara-parabricks The load command will load a default version of Clara Parabricks, unless another version is specified. To see the available versions, type: module spider clara-parabricks Running Clara Parabricks tools The Clara Parabricks container on Rivanna includes many bioinformatics tools for genomics and transcriptomics.
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     HPC, software, bioinformatics    ,