Day 1: Linux/TACC Introduction and Read Mapping
Linux refresher
Using TACC's Lonestar cluster (GVA14)
Introduction to mapping (bowtie, BWA)
Introduction to variant calling (SAMtools)
Documentation
Extras
Introduction to Bioinformatics Prezi
Download Presentation on Mappers, etc. \
Workflow diagram of variant calling
Diagram of Lonestar's directories
Diagram of running a job on Lonestar
Day 2: Calling Genome Variants
Using the Integrative Genomics Viewer (IGV)
Shell Scripting
Mapped read data evaluation (SAMtools)
Installing Linux tools
Identifying mutations in microbial genomes (breseq)
Extras (come early Day 3)
Calling variants in diploid genomes
Annotating variants
Additional topics
Variant calling with GATK
Genome variation in mixed samples (FreeBayes, deepSNV)
Identifying structural variants (SVDetect)
Even More Extras
Download presentation on Advanced Genome Variant Calling|^Barrick_AdvancedGenomeVariantCalling_2012.pdf\
Practical advice - short read re-sequencing data
Day 3: RNA-seq
Differential gene expression analysis
Differential expression with splice variant analysis
Transcriptome assembly & annotation
Extras
non-coding RNA analysis
Day 4: Assembly and Annotation
Genome Assembly
Genome Assembly (velvet)
Genome Annotation (Glimmer3)
Evaluating & Visualizing assemblies
SRA toolkit, UCSC Genome Browser
Custom Genome Databases
Resources
NGS Course Resources
: tool list, file formats & more
Scott's list of linux one-liners
Example BWA alignment script
Exercises