Learning Goals

##Tutorials Organized by Learning Goals

• Computing literacy
• [Shell] (https://github.com/edamame-course/2015-tutorials/blob/master/final/2015-06-22-introduction_to_the_shell.md)
• tmux for remote sessions
• Getting started with GitHub
• Cloud computing
  • Amazon EC2 start-up
  • File transfer to the EC2
• Microbial amplicon analysis
  • Assessing sequencing quality
  • Subsampling a large amplicon dataset for developing an analysis workflow
  • Paired end merging (with PANDASeq)
  • QIIME workflow: rarefaction, building an OTU table, diversity analysis
    1. Part 1: Building an OTU Table
    2. Part 2: Within-Sample Diversity and visualizations
    3. Part 3: Comparative Diversity and OTU table export
  • mothur workflow
• Microbial shotgun metagenome analysis
  • Installing mg tools on the EC2
  • Demo: using seqtk for subsampling a large metagenome dataset for developing an analysis workflow
  • Quality Trimming
  • Digital normalization
  • Assembly with MEGAHit
  • Annotation of assembled reads
  • Xander for targeted gene assembly
• Ecological Statistics with R
  • R basics
  • Visualizations Demo
• Using Databases
  • Local BLAST
  • Using APIs to access NCBI and MG-RAST data

---