/category/bio
Cell Ranger and UVA HPC
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/9.0.1 ModuleVersion Module Load Command cellranger9.0.1 module load cellranger/9.0.1
Cell Ranger ATAC and UVA HPC
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/2.0.0
CellProfiler and UVA HPC
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 and UVA HPC
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/3.0.0rc4 ModuleVersion Module Load Command deeplabcut3.0.0rc4 module load apptainer/1.3.4 deeplabcut/3.0.0rc4 Dockerfile We cannot use the official Docker image on the UVA HPC system because:
Snakemake and UVA HPC
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 snakemake7.24.2 module load snakemake/7.
Workflow Managers and UVA HPC
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 the HPC system 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 and UVA HPC
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/1.17 samtools1.
Amber and UVA HPC
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/24-CUDA-12.2.2 ModuleVersion Module Load Command amber24-CUDA-12.2.2 module load gcc/11.4.0 openmpi/4.1.4 amber/24-CUDA-12.
Bowtie2 and UVA HPC
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 and UVA HPC
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 and UVA HPC
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/30.1 The Backend Configuration In order to allow Cromwell to interact with the HPC system (via SLURM), we need to define a backend to dispatch jobs.
GATK and UVA HPC
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 and UVA HPC
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 and UVA HPC
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 and UVA HPC
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 and UVA HPC
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
