Content Comparison

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• General introduction (SPHS)
  • Introduction to Bioinformatics Prezi
• Linux refresher (SPHS)
  • Step 1: Start somewhere
  • Step 2: Establishing a profile on Lonestar
  • Step 3: Editing files
  • Step 4: Final explanations
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• Using TACC's Lonestar Cluster (SPHS/AR)
  • Diagram of Lonestar's directories
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  • Diagram of running a job on Lonestar
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  • Using SFTP for file browsing on Linux.
• Introduction to next-gen sequencing technologies (SPHS)
  • Official Illumina video | Another Illumina video
  • Broad Center GA Boot Camp
  • GSAF adaptor and barcode sequence resource
• Application: Example genome variant calling pipeline (JB)
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• Evaluating your raw sequencing data (JB/AB)
• Introduction to Mapping and Tutorial
  • Image Removed (JB)
  • Mapping tutorial (bowtie2, BWA) Image Added (JB/GC)
• Tutorial - Start diploid mapping for Day 2

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Day 2: Calling Genome Variants

• Mapping tutorial (bowtie2, BWA) (JB/GC)
• Introduction to genome variation
• Image Removed Image Added (JB)
• Variant calling tutorial (SAMtools) (JB)
• Integrative Genomics Viewer (IGV) tutorial (JB)
• Calling variants in diploid genomes (SPHS)
• Variant calling with GATK (SPHS)
• Annotating variants (SPHS)
• Image Removed Image Added (JB)
• Visualize mapped data at UCSC genome browser (AB)

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