Genomics

• Short read quality and trimming
  • Prepping the computer
  • Data source
  • 1. Copying in some data to work with.
  • 2. Copying data into a working location
  • 3. FastQC
  • 4. Trimmomatic
  • 5. FastQC again
  • 6. Interleave the sequences
• Assembling E. coli sequences with SPAdes
  • Packages to install
  • Getting the data
  • Running an assembly
  • Looking at the assembly
  • Comparing and evaluating assemblies - QUAST
  • Adding in Nanopore data and doing a hybrid assembly
  • Reference-free comparison
• Bacterial genome annotation using Prokka
  • Download and install Prokka
  • Apply Prokka to your just-assembled E. coli genome
  • Install Artemis
  • Viewing the annotated genome

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