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Day 1. Linux/TACC Introduction and Read Mapping

Part 1. Linux/TACC Introduction (SPHS)

• General introduction to Genome Variant Analysis (GVA14)
• Linux refresher and environment setup (SPHS)
  • Step 1: Connecting to and establishing a profile on Lonestar (GVA14)
  • Step 2: Editing files
  • Step 3: Final explanations
  • Linux/Unix command cheat-sheet: 
• Using TACC's Lonestar Cluster (SPHS)
  • Diagram of Lonestar's directories
  • Lonestar tips & tricks cheat-sheet: 
  • Diagram of running a job on Lonestar
  • launcher-creator.py cheat sheet: 
  • Submitting a simple job using launcher_creator.py
• Additional Useful Links (GVA14)

Part 2. Mapping Reads (JB)

• Handout: Variant calling workflow diagram (GVA14) 
• Presentation: Intro to Mapping (GVA14) 
  
• Tutorial: Mapping tutorial (bowtie2, bwa) (GVA14)
• Tutorial: Integrative Genomics Viewer (IGV) (GVA14)
• Bonus: Evaluating and processing raw sequencing data (GVA14) 
• Bonus: Mapped read data evaluation (samstat, SAMtools) (GVA14)

Day 2. Microbial Genome Variation

Part 1. Single-nucleotide variants (JB)

• Presentation: Single-nucleotide variant calling 
  
• Tutorial: SNV calling tutorial (SAMtools) (GVA14)

Part 2. Structural variants (JB)

• Presentation: Structural variant calling 
• Tutorial: SV calling tutorial (SVDetect) (GVA14)
• Tutorial: Advanced variant calling tutorial (breseq) (GVA14)
  

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Day 3: Human Genome Variation

Part 1. Overview and the mechanics of calling variants

• Overview: whole genome and complexity reduction methods (GVA14)
  • Human Trios
  • An introduction to GATK
  • Exomes: capture & metrics
  • Tumor/normal analysis with Virmid (GVA14)
• Samtools mpileup in more detail (optional) 

Part 2. Annotating, filtering, and screening variants; evaluating performance

• Annotating variants with annovar (GVA14)
• Filtering & screening variants
• Evaluating performance
• The importance of validation (discussion)

Day 4: Rare Variant Detection in Populations

Part 1. Sequencing of mixed populations

• Presentation: Sources of errors, and computational methods to improve detection.
• Tutorial: Breseq Identification of Variants in Mixed Population Sequencing (GVA14)
  
• Tutorial: Comparison of mixed population sequencing options (GVA14)

Part 2. Targeted Sequencing of Molecular Indexed Libraries. 

• Presentation: Alternative Library Preparation Methods 
• Presentation: Experimental design
• Tutorial: SSCS Read Generation
• Tutorial: Breseq identification of rare variants within targeted regions
• Discussion: Full results of SSCS sequencing, and use of autocorrelation
  

Resources

• NGS Course Resources Tool List
• GSAF adaptor and barcode sequence resource
• Working on TACC from your Mac or PC
  • Editing files, more detail
• Scott's list of linux one-liners
• Installing Virtual machine & Linux on Windows
• Example BWA alignment script
• Variant calling with GATK (SPHS)
• Visualize mapped data at UCSC genome browser (AB)
• Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
• SRA toolkit and Exercises (AB)
• Shell Scripting (SPHS/AB)
• Installing Linux tools (JB)
• Custom Genome Databases
• Evaluating & Visualizing assemblies (bacterial, SPHS) 
• Genome Assembly Examples (SPHS) 
• Tutorial: Genome Assembly (velvet) (SPHS)
• Visualize mapped data at UCSC genome browser (AB)
• ddRAD (Stacks tutorial: http://evomics.org/wp-content/uploads/2013/03/cesky_2014_RAD_tutorial_updated.pdf) , Tn-Seq?