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Metagenomic Binning Teaching Module

This repository contains teaching materials, demonstrations, and slide decks for teaching a mini Metagenomic Binning Workshop Module at the University of Wisconsin - Madison.

This lesson uses data from Scarborough 2018: Scarborough MJ, Lawson CE, Hamilton JJ, Donohue TJ, Noguera DR. 2018. Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome. mSystems 3:e00221-18.https://doi.org/10.1128/mSystems.00221-18.

Repository Structure:

  • data: raw and polished data used throughout the module
  • instructions: teaching instructions and outlines
  • lessons: lesson demonstrations for module website
  • scripts: analysis scripts
  • slide_decks: teaching slides for concept intros

mcfamodule's People

Contributors

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mcfamodule's Issues

Data Preparation

To Do:

  • Quality Filtering
  • Individual Assemblies
  • Coassemblies
  • Mapping
  • Binning
  • Quality Checks, Draft Genomes, Dereplication

Underlying Learning Objectives

  • Queuing jobs on Condor or for loops?
  • Will have to teach a bit of Condor and submission jobs
  • Docker installations, general installations
  • memory requirements, multi-threading, storage considerations
  • public resources

conceptual slides

Modifying ComBEE session on binning:

  • Motivations, background, what can you learn
  • Terminology
  • General workflow to keep up through the workshop

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