TACC - High Performance Computing for NextGen Sequence Analysis

Oct 8, 2012

Your Instructors

Outline

Linux and Lonestar Refresher Course (9:00-10:00)

• Introduction to TACC DONE
• Linux basics with Lonestar DONE
  • Logging in via SSH
  • Command-line tricks (tab completion and the history)
  • Essential Linux commands
  • Wildcards and special file names
  • Using options with Linux commands
  • Getting help
• Lonestar Essentials
  • The login (or head) nodes
    • Acceptable uses for login nodes
    • What not to use login nodes for
  • Lonestar file systems
    • Diagram of Lonestar's directories DONE
  • Methods for running computing jobs
    • Batch
    • Interactive
      • Running a job on Lonestar DONE
• How to edit files
  • Using nano on the command line
  • Using TextWrangler, Notepad++, or gEdit from a desktop environment
• Finding out what software is available
  • Linux PATHs
  • The module command
    • avail, list, load, swap, unload, key

Break (10:00-10:15)

Delving into HPC-oriented NGS analysis (10:15-11:15)

• Presentation: Survey of the NGS analytical landscape
• Tutorial: Read mapping with BWA and BOWTIE DONE

Speeding up your analyses using parallel computing (11:15-11:50)

• Introduction: Parallelism Strategies (PDF) DONE
• Tutorial: Using threads to speed up mapping on a single compute node DONE
• Tutorial: Using the TACC Parametric Launcher to speed up mapping (or any other natively parallel task) across multiple nodes DONE
  • Bonus example: Using the Launcher to automate Rscript analyses DONE

Set-up for Afternoon (11:50-12:00)

• Pre-flight instructions for Interactive Computing session (please complete before going to lunch) DONE

Lunch (12:00-1:00)

• Please return promptly!

Variant Calling with SAMtools (1:00-1:40)

• Tutorial: Variant calling using SAMtools DONE
  • Calling SNPs and Indels
  • Inspecting alignments supporting a variant using tview
  • Filtering variants
  • Finding summary statistics

Downloading and uploading files using SFTP (1:40-1:50)

• The sftp and scp commands DONE
• Using CyberDuck on the desktop

Review (1:50-2:00)

After-class QA (2:00-2:30)