Instructors: Harriet Alexander, Phil Brooks, and C. Titus Brown
These are the online materials for the environmental metagenomics workshop run at CICESE.
We will be using HackMD to take collective notes throughout the course. If you wish to add to or follow along the HackMD can be found here.
- Read the Critical Assessment of Metagenome Interpretation (CAMI) Paper;
- Read Hu et al. 2016. This is the paper from which we pulled all of our sample data.
- Metagenomic workflows and considerations
- Evaluating short-read quality
- Assembling your short read data set with MEGAHIT
- A brief discussion of workflows & repeatability
- Mapping short reads to the assembly time permitting
- Sourmash compare
- Discussion of CAMI paper
Resources:
See the complete table of contents
The github repository for this workshop is public at https://github.com/ngs-docs/2017-ucsc-metagenomics