Obsolete NGS course materials

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