2016 / October / Metagenomics

This workshop was given on October 12th and 13th, 2016, by Harriet Alexander and C. Titus Brown, at the Scripps Institute of Oceanography.

For more information, please contact Titus directly.

We have an EtherPad for sharing text and asking questions.

Rough schedule:

• Wed, 9am-noon: Amazon Web Services; short reads, QC, and trimming.

• Logging into AWS
• Read quality evaluation and FASTQ trimming (FASTQC, Trimmomatic)
• (Optional) K-mer spectral error analysis and trimming (khmer)

• Wed, 1-4pm: Assembly, annotation, and evaluation.

• Short-read assembly with MEGAHIT
• Advantages and drawbacks to assembly (discussion)
• Evaluating assembly results (mapping rates, mapping viz, etc.)
• Annotating assembly (Prokka)
• Abundance calculations

• Thursday: topics TBD from below, or others:

• Biology and bioinformatics:

• Abundance comparisons between samples
• Taxonomic analysis of reads and assemblies
• Genome binning
• CIRCOS plots
• ShotMap for annotating shotgun reads

• Moar computing:

• Jupyter Notebook or RMarkdown
• git for version control
• Docker execution environments
• Workflow strategies (scripting, make, doit, etc.)
• More Amazon Web Services: EC2, S3, ...?

• Miscellany:

• Visualizing assembly graphs
• MinHash sketches for comparing genomes and metagenomes
• Tricks with sequences using Python libraries (screed & khmer)

Tutorials:

• Welcome!
  • 1. Learning goals
  • 2. Safe space and code of conduct
  • 3. Instructor introductions
  • 4. Amazon and cloud computing - why?!
  • 5. Sticky notes and how they work... + Minute Cards
• Starting up an Amazon Web Services machine
  • Start here: boot
  • Full table of contents:
• Indices and tables
• Short read quality and trimming
  • Prepping the computer
  • Installing some software
  • Running Jupyter Notebook
  • Data source
  • 1. Copying in some data to work with.
  • 1. Copying data into a working location
  • 2. FastQC
  • 3. Trimmomatic
  • 4. FastQC again
• K-mer Spectral Error Trimming
  • Why (or why not) do k-mer trimming?
• Run the MEGAHIT assembler
  • While the assembly runs...
  • After the assembly is finished
• Annotation with Prokka
  • Installing Prokka
  • Running Prokka
  • References
• Gene Abundance Estimation with Salmon
  • Installing Salmon
  • Running Salmon
  • Working with count data
  • Plotting the results
  • References
• Day 2 - installation instructions
  • Running Jupyter Notebook

Technical information

The github repository for this workshop is public at https://github.com/ngs-docs/2016-metagenomics-sio

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LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

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