Genome Sequence Analysis

Knowledge:

• Second generation sequencing technology
  • Library construction (theoretical level)
  • Sequencing by synthesis
  • Bridge amplification
  • Base calling
  • Newer developments (third generation)
• Applications of second generation sequencing technology
  • Overview of how second generation sequencing can be used / adapted to answer various biological questions
  • Whole-genome DNA sequencing
  • RNA sequencing
• Analysis strategies and workflows for second generation sequencing data
  • Filtering and quality evaluation of raw reads
  • Mapping of sequencing reads onto a reference genome
  • Sequencing coverage
  • Variant and genotype calling from whole-genome DNA sequencing data
  • Gene/transcript expression quantification, de novo transcript reconstruction and differential expression analysis using RNA sequencing data
• Basic knowledge of the various statistical/computational approaches and tools used when dealing with sequencing data and how and why these differ between sequencing applications
• Familiarity with of state-of-the-art statistical and computational approaches for dealing with whole-genome sequencing data for variant calling and RNA-sequencing data for gene transcript expression quantification and differential expression analysis
• Basic knowledge of the issues and potential problems with second generation sequencing data and how to deal with those
• Basic knowledge of impact of study designs and how to avoid and deal with batch effects 
• Genomic annotation of sequencing data and genome browsers
   

Skills:

• Identify differentially expression of gene transcripts between biological samples of different types or conditions
• Identify mutations in an experimental sample by variant calling
• Design and carry out genetic experiments to relate identified variants with mutant phenotypes

Competences:

• Critically evaluate results of second generation sequencing experiments from different perspectives (molecular biology, bioinformatics, genetics)
• Independently analyze and interpret whole-genome DNA sequencing data and RNA-sequencing data