We will meet in Room 7.306 of Robert Lee Moore Hall (RLM). We encourage you to use the computers provided in the classroom for these tutorial, but you may also bring your personal laptops.
Etherpad
You can jot questions or command lines to share with the class here: https://etherpad.mozilla.org/V1EIko9FS5
Your Instructors
Name | Initials | Affiliation | Expertise |
|---|---|---|---|
SPHS | Director GSAF | Everything, if loosely defined (but especially | |
JB | Molecular Biosciences | Microbes, Perl, C++, Mac, breseq, Miscellanea | |
Dan Deatherage | DD | Barrick Lab | Unix, Python, NGS Library Prep, Capture, Rare variants |
We acknowledge a great deal of help with creating these web pages and materials from other instructors of the Intro to NGS Bioinformatics course most recently taught in May 2013.
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)
Day 3: Human Genome Variation
Part 1. Overview and the mechanics of calling variants
- Overview: whole genome and complexity reduction methods (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
- 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?
