biovcnet/topic-metagenomics

A repository for the lessons and notebooks used for Binder tutorials

TOPIC: Metagenomics

Prerequisites for topic

• A working Unix environment
• Experience with the command line

Overview

This topic will cover:

• how to use shotgun metagenomic sequencing technologies to answer biological questions
• the methodologies used to perform metagenomic studies on the taxonomy, function, evolution, and ecology of microorganisms
• the intricacies of the specific tools and databases that can used for varying levels of specificity.

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Released Lessons

Lesson 1: What is metagenomics?

• [Presentation Slides] and [Presentation Video] by Eric Collins
• What kinds of questions can metagenomics be used to answer?
• Is metagenomics right for me?
• Yay! You got data! Now what?

Demo 1.1: Quality Control using FastQC and MultiQC

• [Video Tutorial] by Alexis Marshall
• 
• [Bash script]
• Programs used:
  • fastqc
  • multiqc

Lesson 2: Taxonomic Classification using k-mers

• [Presentation Slides] and [Presentation Video] by Eric Collins
• The power of k-mers
• Choosing a k-mer classifier

Demo 2.1: Taxonomic Classification and Adapter Trimming using k-mers

• [Video Tutorial] by Eric Collins
• 
• [Bash script]
• Programs used:
  • kraken2
  • bbduk
  • krona

Demo 2.2: Adapter and quality trimming using trimmomatic

• [Video Tutorial] by Ella Sieradzki
• 
• [Bash script]
• Programs used:
  • fastqc
  • multiqc
  • trimmomatic

Lesson 3: Taxonomic Classification using MinHash sketches

• [Presentation Slides] and [Presentation Video] by Eric Collins
• The Jaccard Index
• How does MinHash work?
• How do Bloom filters work?
• Choosing a MinHash sketcher

Demo 3.1: Taxonomic Classification using sourmash and sendsketch, and quality trimming using bbduk

• [Video Tutorial] by Eric Collins
• 
• [Bash script]
• Programs used:
  • sourmash
  • sendsketch
  • bbduk

Lesson 4: Read mapping and read taxonomic classification

• [Presentation Slides] and [Presentation Video] by Luis Valentin and Ella Sieradzki
• 
• How does mapping work?
• Choosing a metagenomic read mapper
• The Burrows-Wheeler transform and using bowtie2

Demo 4.1: Mapping reads with bbtools

• [Video Tutorial] by Ella Sieradzki
• [Bash script]
• Programs used:
  • bbmap
  • bbwrap
  • bbsplit

Demo 4.2: Taxonomic classification of reads

• [Video Tutorial] by Ella Sieradzki
• 
• Programs used:
  • Kaiju
  • Centrifuge

Lesson 5: Genome and Metagenome Assembly

• [Presentation Slides]
• Sequencing Statistics
• Overlap-Layout-Consensus assembly
• de Bruijn Graph assembly
• Assembly software

Demo 5.1: Genome assembly

• 
• [Bash Script]
• Programs used:
  • bbduk
  • tadpole
  • spades
  • statswrapper

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Planned Lessons

Lesson 6: Assembly Quality and Statistics

• 
• How do you determine the quality of an assembly?
• Choosing an assembly quality metric
• Demo using QUAST, etc.

Lesson 7: Assembly Visualization

• What is an assembly graph useful for?
• Demo using Bandage

Lesson 8: Binning

• How does metagenomic binning work?
• Choosing a metagenomic binner
• Demo using metabat2, CONCOCT, etc.

Lesson 9: Evaluating bins

• What are single-copy core genes?
• Choosing a bin evaluation tool
• Demo using CheckM, etc.

Lesson 10: Phylogenomics

• What are single-copy core genes?
• Basics of sequence alignment
• Basics of phylogenetic tree construction
• Demo using GToTree, GTDBtk, etc.

Lesson 11: Workflows -- Putting it all together

• A review of existing workflows
• Why you probably shouldn’t invent your own workflow
• What to do when you inevitably decide to invent your own workflow anyway
• Demo using SnakeMake, Nextflow, etc.

Lesson 12: Workflows: Online Portals

• Anvi’o
• MGnify
• MG-RAST
• Galaxy
• JGI
• Cyverse
• KBase
• etc