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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 ###Overarching Learning Goals

1. Increase computing literacy
2. Develop proficiency in cloud computing
3. Analyze microbial amplicon sequences
4. Analyze microbial shotgun metagenome sequences
5. Apply ecological statistics to analyze and interpret microbial sequencing data
6. Access resources provided by public sequence databases

• Computing literacy
• [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
• 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
  • Subsampling a large metagenome dataset for developing an analysis workflow
  • Quality Trimming
  • Digital normalization
  • Assembly with MEGAHit
  • Annotation of assembled reads
• Ecological Statistics with 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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