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Ashley Shade edited this page Jun 5, 2015 · 42 revisions

Welcome to the EDAMAME 2015-tutorials wiki!

###Tutorials

###Tutorials by topic

  • Getting around at the command line
  • Terminal basics
  • 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
    • mothur workflow: rarefaction, building an OTU table, diversity analysis
  • Shotgun metagenome analysis
    • 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

###Tutorials by schedule ###2015 Schedule

EDAMAME : Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology at Michigan State University

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