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Research and Teaching IT Support

Samtools

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Research and Teaching IT Support

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Getting Started
Getting Started
- Quick Start
- Access
  Access
- Data transfer
  Data transfer
- Software
  Software
  - Software Overview
  - onDemand
    onDemand
    
    Available Apps
    
    OnDemand HPC Desktop
    
    Open OnDemand
    
    Ood file manager
    
    Ood shell
  - Software environments
    Software environments
    
    SBGrid
    
    Containers
    Containers
    
    AFNI (Analysis of Functional NeuroImages)
    
    AlphaFold
    
    Ansys Fluent
    
    Bohra
    
    CCP4
    
    Circlator
    
    GLOBEClaritas
    
    ColabFold
    
    Connectome Workbench
    
    DeepLabCut
    
    DeepPoseKit
    
    Dorado
    
    FSL
    
    Gubbins
    
    Guppy (GPU)
    
    HUMAnN 3.0
    
    MATLAB
    
    Ollama
    
    Openprose
    
    Samtools
    
    Space Ranger
    
    TBProfiler
    
    Whisper (speech-to-text)
    
    xdsguI
    
    Modules
    Modules
    
    4ti2
    
    Macaulay2
    
    Mathematica
    
    Modules (LMOD)
    
    Self managed
    Self managed
    
    Apptainer (Singularity)
    
    Conda/Mamba
    
    Renv (R package environments)
    
    Shells (bash, zsh, fish, tcsh)
    
    Spack
    
    Venv (Python virtual environments)
- Running Jobs
  Running Jobs
  - Current utilisation
  - Job Efficiency
  - Interactive Jobs
  - Slurm Job Scheduling
  - Slurm examples
    Slurm examples
    
    Array Jobs
    
    Dependent Jobs
    
    Using a GPU with Slurm
    
    Heterogeneous Jobs
    
    Interactive Jobs
    
    Using Python with Slurm
    
    Using R with Slurm
- Workflows
  Workflows
  - Nextflow
  - Project setup
    Project setup
    
    Project setup
    
    Bioinformatics software
    
    Rstudio
General
General
- Research HPC Cluster (Aoraki)
- Announcements
  Announcements
  - April 2025 Maintenance
  - November 2024 Maintenance
- Guidelines
  Guidelines
- Changelogs
  Changelogs
- FAQ
  FAQ
  - How much disk storage am I using?
  - Exceeding quota
Storage
Storage
- Storage Overview
- File permissions
- Data Locations
  Data Locations
  - Hcs
  - Homes
  - Projects
  - Weka

Samtools¶

Samtools 1.20 is natively installed for all users

Terminal

samtools --version

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