Welcome to 2014 MSU QB summer microbial genomics tutorial

Day	Schedule
Wed 8/13	2-3pm: Get started with Amazon EC2 3-5pm: Read mapping and variant calling
Thu 8/14	2-5pm: Genome assembly

Sequencing technologes

• 454
• Illumina
• PacBio
• NanoPore

Resources

• Biostar

  A high quality question & answer Web site.

• SEQanswers

  A discussion and information site for next-generation sequencing.

• Software Carpentry lessons

  A large number of open and reusable tutorials on the shell, programming, version control, etc.

Table Of Contents

• Amazon Web Services instructions
  • Start up an EC2 instance
  • Logging into your new instance “in the cloud” (Mac or Linux version)
  • Logging into your new instance “in the cloud” (Windows version)
  • Terminating (shutting down) your EC2 instance
  • Starting up a custom operating system
• Variant calling
  • Booting an Amazon AMI
  • Do the mapping
  • Visualizing alignments
  • Counting alignments
  • Calling SNPs
  • Questions/discussion items
• Assembling E. coli sequences with Velvet
  • Booting an Amazon AMI
  • Running an assembly
  • Comparing and evaluating assemblies - QUAST
  • Searching assemblies – BLAST
  • Questions and Discussion Points