Short-read genomics in the Amazon cloud

This course covers short-read genomics as applied to modern short-read datasets.

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 short-read massively parallel sequencing.
• Setting up and accessing your own Linux virtual machine in the Amazon cloud computing environment.
• Accessing the virtual machine using the NX client.
• Illumina QC.
• Remapping reads to a reference sequence.
• Visualisation.
• Variant calling.
• Identifying missing genes.
• Extraction and assembly of unmapped reads.
• Basic annotation using PFAM, RAST and Blast.
• Assembly of complete genomes de-novo.
• Annotation.
• Comparative analysis of several datasets.

Biologists and other researchers are more and more likely to encounter short-read datasets in their everyday research. 

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