Course materials available at https://wikis.utexas.edu/display/bioiteam/SSC+Intro+to+NGS+Bioinformatics+Course

Topics

1. Linux/TACC Introduction and Read Mapping
   • Shell Scripting
   • Installing Linux tools
   • Introduction to mapping (bowtie, BWA)
   • Introduction to variant calling (SAMtools)
2. Calling Genome Variants
   • Using the Integrative Genomics Viewer (IGV)
   • Mapped read data evaluation (SAMtools)
   • Identifying mutations in microbial genomes (breseq)
   • Calling variants in diploid genomes
   • Annotating variants
   • Variant calling with GATK
   • Genome variation in mixed samples (FreeBayes, deepSNV)
   • Identifying structural variants (SVDetect)
3. RNA-seq
   • Differential gene expression analysis
   • Differential expression with splice variant analysis
   • Transcriptome assembly & annotation
4. Assembly and Annotation
   • Genome Assembly
   • Genome Assembly (velvet)
   • Genome Annotation (Glimmer3)
   • Evaluating & Visualizing assemblies
   • SRA toolkit, UCSC Genome Browser
   • Custom Genome Databases