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Welcome to the EDAMAME 2015-tutorials wiki!

###Tutorials

• Tutorials organized by topic
  
• [Tutorials organized by 2015 schedule] (#schedule)
  

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###Tutorials by topic

• Getting around at the command line, computing tips
• [Terminal basics] (https://github.com/edamame-course/2015-tutorials/blob/master/draft/josh/introduction_to_the_shell.md])
• tmux for remote sessions
• Automation and text matching tips
• Cloud computing
  • Amazon EC2 start-up
  • File transfer to the EC2
• 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
• Shotgun metagenome analysis
  • Installing mg tools on the EC2
  • Subsampling a large metagenome dataset for developing an analysis workflow
  • Quality Trimming
  • Digital normalization
  • Assembly with MEGAHit
  • Annotation of assembled reads
• R
  • R basics
  • Advanced R
  • R visualizations
• Using Databases
  • Local BLAST
  • Using APIs to access NCBI and MG-RAST data

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###Tutorials by schedule ###2015 Schedule

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