# 2017 DIBSI Metagenomics Workshop at UC Davis Lead Instructors: Harriet Alexander and C. Titus Brown Co-Instructors: Jessica Blanton, Adelaide Rhodes, Shawn Higdon, Jessica Mizzi, Phillip Brooks, Veronika Kivenson These are the online materials for the environmental metagenomics workshop run as part of the Data Intensive Biology Summer Institute at UC Davis ([DIBSI](http://ivory.idyll.org/dibsi/)). We will be using HackMD to take collective notes throughout the course: [HackMD](https://hackmd.io/MzBmE4FYCMA4HYC08BMtSICwFMCGA2RWTfXRSABnAsxXAGNhJRcg). ## Monday, Day 1: 11am: Meet in Valley Hall (room TBA), setup, and introductions. * [Logging into the cloud (XSEDE Jetstream)](jetstream/boot.html) Noon - 1:15: Lunch 1:15 - 2pm: Group meeting with all of DIBSI 2pm - 4pm: * [Working on Command Line](command-line.html) * [Command Line Blast](running-command-line-blast.html) Homework: *Skim* the [Critical Assessment of Metagenome Interpretation (CAMI) Paper](http://www.biorxiv.org/content/biorxiv/early/2017/01/09/099127.full.pdf) ## Tuesday, Day 2: 9am - Noon: * [Introduction to dataset we will be using]() * [Evaluating your short-read data set quality](quality.html) Noon - 1:15: Lunch 1:15 - 4pm: * Lecture about assembly from Titus Brown * Trying quality trimming and assembly with your own data! ## Wednesday, Day 3: 9am - Noon: * [Assembling your short read data set with MEGAHIT](assemble.html) * [Quickly searching and comparing your samples with sourmash](sourmash.html) Noon - 1:15: Lunch 1:15 - 4pm: * [Mapping short reads to the assembly](mapping.html) *time permitting* * [Binning genomes out of your metagenome](binning.html) ## Thursday, Day 4: 9am - Noon: * [Annotating your dataset with Prokka](prokka_tutorial.html) * [Quantifying abundance across samples with Salmon](salmon_tutorial.html) Noon - 1:15: Lunch 1:15 - 4pm: * [Anvi'o](anvio.html) * [A brief discussion of workflows & repeatability](workflows.html) ## Friday, Optional Day 5: TBD (plotting, visualization, jupyter notebooks...) [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 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