Welcome to Metagenomics One Day Crash Course!

Contents:

These are the tutorials that are a merge of my perspective of what I wish someone would have showed me in less than 6 hours when I was a total newbie to metagenomic sequencing analysis.

Three main tutorial sections:

• Unix Shell
• Getting data
• Running a program
• Fungene and BLAST

Resources:

Practical Computing for Biologist

Bioinformatics Programming with Python

Effective Computation in Physics

• What is the shell how do I access the shell?
• Access via Terminal
  • To open a terminal
• The Example: Manipulating Experimental Data Files
• Let’s get started
• Searching files
• Finding files

• Fetching Data with the NCBI API
  • Learning objectives
  • Getting the data
  • Understand the Data
  • Understand the gene of interest (based on a literature)
  • Find more genes of interest (based on NCBI)
  • Determine the list of genes to build a reference database
  • Download the associated sequence for genes
  • Understanding NCBI’s API
  • Bringing this to the command line
  • Scaling up sequencing downloading from a list
  • Build your giant database
  • Under the hood
  • A challenge exercise

• Running a bioinformatic program
  • Learning objectives
  • Install BLAST
  • Running BLAST
  • Automation exercise
  • Getting the best hit
  • For loop exercise - best hits
  • More practice executing a program/script
  • Adding annotations
  • Conclusion

• Fungene is FUN!
  • Learning objectives
  • Install BLAST - Students working on a shared computer can likely skip this step
  • Running BLAST
  • Automation exercise
  • Getting the best hit
  • More practice executing a program/script
  • Adding annotations
  • Conclusion