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
  • Computing workflows for biologists - paper

• Cloud computing

  • Amazon EC2 start-up
  • File transfer to the EC2
  • Getting started with the EC2 - from Angus

• Microbial amplicon analysis

  • Assessing sequencing quality with FastQC (bonus: intro to automation, installing software on the EC2)
  • Subsampling a large amplicon dataset for developing an analysis workflow
  • Firing up the QIIME AMI
  • QIIME workflow overview
  • QIIME tutorial
  • mothur workflow

• Microbial shotgun metagenome analysis

  • Examples of installing mg tools on the EC2
  • Demo: using seqtk for subsampling a large metagenome dataset for developing an analysis workflow
  • metaG sequencing preprocessing, quality control, and trimming
  • Digital normalization
  • Assembly with MEGAHit
  • Evaluating assembly
  • Estimating abundance from metagenomes
  • Binning assemblies
  • Annotation of assembled reads
  • Xander for targeted gene assembly

• Ecological Statistics with R

  • R basics
  • Visualizations Demo
  • Quick intro to R for comparative (beta) diversity

• Using Databases

  • Local BLAST
  • Using APIs to access NCBI and MG-RAST data
  • Getting data from NCBI

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