Genomics

This course covers genomic analysis as applied to modern short and long read datasets (100's bp through to multi kilobase reads).

This course assumes you have attended the Unix and Perl workshop and/or have previous experience with the Linux command line.

The target audience for the course is anyone wanting further training in bioinformatics: PhD, post-docs, technicians, and faculty staff.

 

Course content

  • The theory behind massively parallel sequencing.
  • Setting up and accessing your own Linux virtual machine in a cloud computing environment.
  • Accessing the virtual machine
  • Illumina QC
  • Remapping reads to a reference sequence
  • Visualisation
  • Variant calling
  • Identifying missing genes
  • Extraction and assembly of unmapped reads
  • Basic annotation using Prokka and other tools
  • Assembly of complete genomes de-novo
  • Comparative analysis of several datasets.

 

Biologists and other researchers are more and more likely to encounter Illumina or other short-read genomics datasets in their everyday research. An introduction to PacBio and Oxford Nanopore datasets will also be provided. Participants will be able to take the techniques and skills they learn back to their groups to continue making their own research easier and more effective.

 

Course details

Dates: Feb. 2018 (TBC)
Time: 1:30 – 4:30pm
Duration: Three weeks (half a day per week plus homework).
Instructors: Paul O'Neill
Prerequisites: Participants must be comfortable with the Linux command line.
Location: Hatherley B12
Streatham Campus
University of Exeter

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