UVA Research Computing

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  • Amber on Rivanna

    Description A suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community.
    Software Category: bio For detailed information, visit the Amber website. Local support is not available. Available Versions The current installation of Amber lags behind the latest release due to license restrictions. To find the available versions and learn how to load them, run: module spider amber The output of the command shows the available Amber module versions. For detailed information about a particular Amber module, including how to load the module, run the module spider command with the module’s full version label.

  • Bowtie2 on Rivanna

    Description Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Software Category: bio For detailed information, visit the Bowtie2 website. Available Versions The current installation of Bowtie2 incorporates the most popular packages.
  • BWA on Rivanna

    Description Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. BWA provides three alignment algorithms: BWA-backtrack BWA-SW BWA-MEM The BWA-backtrack algorithm is exclusively used for short sequence reads up to 100bp, the latter two can be used for sequence reads of up to 1MB. The BWA-MEM algorithm can also be used for high-quality short Illumina sequence reads (< 100bp) in many cases with better performance compared to the original BWA-backtrack algorithm. Therefore, the more universal BWA-MEM algorithm is recommended as a starting point for most alignment scenarios.
  • CellProfiler on Rivanna

    Description CellProfiler is an image processing package to generate morphometric measurements. Software Category: bio For detailed information, visit the CellProfiler website. Available Versions To find the available versions and learn how to load them, run: module spider cellprofiler The output of the command shows the available CellProfiler module versions. For detailed information about a particular CellProfiler module, including how to load the module, run the module spider command with the module’s full version label. For example: module spider cellprofiler/2.2.0 function getToolchain(parent) { return parent } Module Version Module Load Command cellprofiler 2.
  • NCBI Blast on Rivanna

    Description Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. Software Category: bio For detailed information, visit the NCBI Blast website. Available Versions To find the available versions and learn how to load them, run: module spider blast The output of the command shows the available NCBI Blast module versions. For detailed information about a particular NCBI Blast module, including how to load the module, run the module spider command with the module’s full version label. For example: module spider blast/2.
  • SAMTools on Rivanna

    Description SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Software Category: For detailed information, visit the SAMTools website. Available Versions The current installation of SAMTools incorporates the most popular packages. To find the available versions and learn how to load them, run: module spider samtools The output of the command shows the available SAMTools module versions. For detailed information about a particular SAMTools module, including how to load the module, run the module spider command with the module’s full version label. For example: module spider samtools/1.
  • SmrtLink on Rivanna

    Description PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided Software Category: For detailed information, visit the SmrtLink website. Available Versions To find the available versions and learn how to load them, run: module spider smrtlink The output of the command shows the available SmrtLink module versions. For detailed information about a particular SmrtLink module, including how to load the module, run the module spider command with the module’s full version label.