/category/bio

  • Cell Ranger ATAC on Rivanna

    Description Cell Ranger ATAC is a set of analysis pipelines that process
    Chromium Single Cell ATAC data.
    Software Category: bio
    For detailed information, visit the Cell Ranger ATAC
    website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider cellranger-atac The output of the command shows the available Cell Ranger ATAC
    module versions.
    For detailed information about a particular Cell Ranger ATAC
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider cellranger-atac/2.0.0 ModuleVersion Module Load Command cellranger-atac2.0.0 module load cellranger-atac/2.

  • Cell Ranger on Rivanna

    Description A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
    Software Category: bio
    For detailed information, visit the Cell Ranger
    website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider cellranger The output of the command shows the available Cell Ranger
    module versions.
    For detailed information about a particular Cell Ranger
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider cellranger/8.0.0 ModuleVersion Module Load Command cellranger8.0.0 module load cellranger/8.0.0

  • CellProfiler on Rivanna

    Description CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
    Software Category: bio
    For detailed information, visit the CellProfiler
    website.
    Available Versions The current installation of CellProfiler
    incorporates the most popular packages. 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:

  • DeepLabCut on Rivanna

    Description DeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks.
    Software Category: bio
    For detailed information, visit the DeepLabCut
    website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider deeplabcut The output of the command shows the available DeepLabCut
    module versions.
    For detailed information about a particular DeepLabCut
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider deeplabcut/2.2.1.1-anipose ModuleVersion Module Load Command deeplabcut2.2.1.1-anipose module load apptainer/1.2.2 deeplabcut/2.2.1.1-anipose Dockerfile We cannot use the official Docker image on Rivanna because:

  • Snakemake on Rivanna

    Description The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
    Software Category: tools For detailed information, visit the Snakemake
    website.
    Available Versions The current installation of Snakemake
    incorporates the most popular packages. To find the available versions and learn how to load them, run:
    module spider snakemake The output of the command shows the available Snakemake
    module versions.
    For detailed information about a particular Snakemake
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider snakemake/7.24.2 ModuleVersion Module Load Command snakemake7.

  • Workflow Managers on Rivanna

    Workflow managers are used to create reproducible and scalable analysis pipelines. These managers are useful when you have a series of scripts that you want to tie together in the form of a pipeline.
    The most popular workflow managers on Rivanna are listed below:
    Snakemake Snakemake is a workflow management system written in Python. It integrates with both conda environments and singularities. Cromwell Cromwell is a Workflow Management System geared towards scientific workflows Nextflow Nextflow enables scalable and reproducible scientific workflows using software containers

  • 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: bio
    For detailed information, visit the Samtools
    website.
    Available Versions 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/1.17 ModuleVersion Module Load Command samtools1.17 module load samtools/1.

  • Amber on Rivanna

    Description Amber (originally Assisted Model Building with Energy Refinement) is software for performing
    molecular dynamics and structure prediction.
    Software Category: chem
    For detailed information, visit the Amber
    website
    Local support is not available.
    Available Versions 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. For example:
    module spider amber/22.0 ModuleVersion Module Load Command amber22.0 module load gcc/11.

  • 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.

  • Cromwell on Rivanna

    Description Cromwell is a Workflow Management System geared towards scientific workflows.
    Software Category: tools For detailed information, visit the Cromwell
    website.
    Available Versions The current installation of Cromwell
    incorporates the most popular packages. To find the available versions and learn how to load them, run:
    module spider cromwell The output of the command shows the available Cromwell
    module versions.
    For detailed information about a particular Cromwell
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider cromwell/30.1 ModuleVersion Module Load Command cromwell30.1 module load cromwell/30.

  • GATK on Rivanna

    Description The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
    to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
    with a primary focus on variant discovery and genotyping as well as strong emphasis on
    data quality assurance. Its robust architecture, powerful processing engine and
    high-performance computing features make it capable of taking on projects of any size.
    Software Category: bio
    For detailed information, visit the GATK
    website.
    For a GitHub reference, visit: https://github.com/broadinstitute/gatk
    Available Versions The current installation of GATK
    incorporates the most popular packages. To find the available versions and learn how to load them, run:

  • 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 The current installation of NCBI Blast
    incorporates the most popular packages. 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.

  • Picard on Rivanna

    Description A set of tools (in Java) for working with next generation sequencing data in the BAM format. Software Category: bio
    For detailed information, visit the Picard
    website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider picard The output of the command shows the available Picard
    module versions.
    For detailed information about a particular Picard
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider picard/2.27.5 ModuleVersion Module Load Command picard2.27.5 module load picard/2.27.5

  • 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: bio
    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.

  • WDLTool on Rivanna

    Description A Java command-line tool co-developed with WDL that performs utility functions, including syntax validation and generation of input JSON templates.
    Software Category: tools For detailed information, visit the WDLTool
    website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider wdltool The output of the command shows the available WDLTool
    module versions.
    For detailed information about a particular WDLTool
    module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider wdltool/0.14 ModuleVersion Module Load Command wdltool0.14 module load wdltool/0.14