Instructors: Harriet Alexander, Phillip Brooks, and C. Titus Brown
TAs: Luiz Irber, Shannon Joslin, Taylor Reiter
These are the online materials for a metagenomics workshop hosted by Marilou Sison-Mangus at UC Santa Cruz on April 22nd and April 23rd, 2017.
Logging into the cloud (XSEDE Jetstream)
Evaluating your short-read data set quality
Assembling your short read data set with MEGAHIT
Binning genomes out of your metagenome
Quickly searching and comparing your samples with sourmash
Annotating your short-read data set with Prokka
Quantifying abundance across samples with Salmon
A brief discussion of workflows & repeatability
Resources:
What next? Workflows; CAzy, KEGG; etc.
The github repository for this workshop is public at https://github.com/ngs-docs/2017-ucsc-metagenomics