# 2017 Metagenomics workshop at UC Santa Cruz

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.

[Etherpad](https://public.etherpad-mozilla.org/p/UCSC_metagenomics)

## Day 1: Noon to 5pm

[Logging into the cloud (XSEDE Jetstream)](jetstream/boot.html)

[Evaluating your short-read data set quality](quality.html)

[Assembling your short read data set with MEGAHIT](assemble.html)



## Day 2: Morning (9am - noon)

[Software install for day 2](day2-install.html)

[Binning genomes out of your metagenome](binning.html)

[Quickly searching and comparing your samples with sourmash](sourmash.html)


## Day 2: Afternoon (1:15pm - 5pm)

[Annotating your short-read data set with Prokka](prokka_tutorial.html)

[Quantifying abundance across samples with Salmon](salmon_tutorial.html)

[A brief discussion of workflows & repeatability](workflows.html)

[What next?](whatnext.html)

Resources:

[SEQ Answers](http://seqanswers.com/)

[Biostars](https://www.biostars.org/)

[Data Carpentry](http://www.datacarpentry.org/)

[DIB Summer Institute](http://ivory.idyll.org/dibsi/)

## Undone

[Circos for viz](circos_tutorial.html)

What next? Workflows; CAzy, KEGG; etc.

<!-- See [the complete table of contents](toc.html) -->

## Technical information

The github repository for this workshop is public at
https://github.com/ngs-docs/2017-ucsc-metagenomics