Oct 8, 2012
Location: ACES 2.402 ; 9 am - 2 pm (CDT)
Your Instructors
Name |
Initials |
Affiliation |
Expertise |
---|---|---|---|
Matt Vaughn |
MWV |
Manager, TACC Life Sciences |
|
John Fonner |
JF |
Research Associate, TACC Life Sciences |
|
TBD |
TBD |
Research Engineer, TACC Life Sciences |
|
Outline
Linux and Lonestar Refresher Course (9:00-9:45)
- Introduction to TACC
- Linux basics with Lonestar
- 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
- Methods for running computing jobs
- Batch
- Interactive
- The login (or head) nodes
- 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
Delving into HPC-oriented NGS analysis (9:45-10:30)
- Presentation: Survey of the NGS analytical landscape
- Tutorial: Read mapping with BWA and BOWTIE
Speeding up your analyses using parallel computing (10:30-11:45)
- Overview of parallelism strategies
- Threading
- Message passing
- Distributed computing
- Using threads to speed up mapping on a single compute node
- Using the TACC Parametric Launcher to speed up mapping (or any other natively parallel task) across multiple nodes
Set-up for Afternoon (11:45-12:00)
- Pre-flight instructions for Interactive Computing session (please complete before going to lunch)
Lunch
Interactive computing using TACC Lonestar (12:00-1:30)
More NGS analysis with HPC
- Tutorial: Variant calling using SAMtools
- Calling SNPs and Indels
- Filtering and converting to VCF
- Inspecting alignments supporting a variant using tview
- Bonus material: Variant calling using GATK