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)


Technical information

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

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.