Workshop

The chapters in this section of the site will lead you through each step of the workshop. Please work through these steps in order and, if you get stuck, please ask one of the lecturers or demonstrators for help.

• 6  Inspect Read Quality: Assessing the quality of sequence read data for your isolate
• 7  Clean Raw Read Data: Prepare your sequencing read data for assembly
• 8  Map Reads to the Genome, 9  Visualise the Mapping, and 10  Find Sequence Variants: Identify sequence variants (SNPs, Single Nucleotide Polymorphisms) between your isolate and a reference genome, and against another study isolate
• 11  Assemble the ERR531380 Genome: Assess genome assembly quality for your isolate
• 12  PubMLST Classification Use pubMLST to classify your isolate
• 13  Building a Phylogenetic Tree and 14  Visualising the Phylogenetic Tree: Build and visualise a phylogenetic tree of isolates from the study
• 15  Tracing the Source: Use your data to draw conclusions about nosocomial transmission