# Next-Gen Sequence Analysis Workshop (2019) These are the schedule and classroom materials for the [ANGUS workshop at UC Davis](http://ivory.idyll.org/dibsi/ANGUS.html), which will run from July 1st to July 13th, 2019. ANGUS is part of the 2019 [Data Intensive Biology Summer Institute](http://ivory.idyll.org/dibsi/). This workshop runs under a [Code of Conduct](code-of-conduct.html). Please respect it and be excellent to each other! We hope that we can respect each other by following these [guidelines & expectations](guidelines-expectations.md). > **Please [submit your feedback here](https://docs.google.com/forms/d/e/1FAIpQLSc1G8J6KQlkkrkVbH5U1H1EdkomFbCS3qzvwlwEyaQSTFHFsg/viewform) on any aspect of the workshop.** *We encourage feedback from everyone involved in the workshop in any capacity* Twitter hash tag: [#dibsi2019](https://twitter.com/search?f=tweets&q=%23dibsi2019&src=typd) ## 3 Rooms & lead instructors! Room Mexía will be led by [Rocio Martinez-Nunez](https://twitter.com/rociotmartinez?lang=en) and [Taylor Reiter](https://twitter.com/ReiterTaylor?lang=en), in 1043 Valley. Room Lovelace will enjoy the leadership of [Chissa Rivaldi](https://twitter.com/Powerofcheez?lang=en) and [Mike Lee](https://twitter.com/AstrobioMike?lang=en), in 1041 Valley. Room Conway will be led by [Sateesh Peri](https://twitter.com/perisateesh?lang=en) & [Marian Schmidt](https://twitter.com/micro_marian?lang=en), in 2020 Valley. ## Schedule, in brief: **Monday, July 1st, 2019:** * **1:30-2:20pm:** [Welcome to ANGUS 2019 slides](http://bit.ly/2019_ANGUS_Welcome) * **2:20-2:30pm:** BREAK * **2:30-3:30pm:** Room Welcomes * **3:30-3:45pm:** BREAK * **3:45pm-5:00pm:** [Introduction to cloud computing and a motivating example](cloud_computing_intro.md) * **5:00pm:** DONE **Tuesday, July 2nd, 2019:** * **9:00-10:20am:** [Introduction to the Shell](shell_intro/index.html) * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** [Introduction to the Shell](shell_intro/index.html) * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Lisa K Johnson](https://twitter.com/monsterbashseq?lang=en): [Intro to Modern Sequencing Practices](https://docs.google.com/presentation/d/1HCGTma7OUTeiepuKQ1h-Sya3L2HLnAAoFGpZO52GPCk/edit#slide=id.p) - [view recording!](https://youtu.be/mBVdRRUcqZI) * **2:00-2:10pm:** BREAK * **2:15-5:00pm:** Poster session & Ice Cream Social (with dairy-free options!) * **5:00pm:** DONE **Wednesday, July 3rd, 2019:** * **9:00-9:15am:** **Meet in Lecture Room (1030) for quick meeting** * **9:20-10:20am:** Wrapping up [Introduction to the Shell](shell_intro/index.html) * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** Wrapping up [Introduction to the Shell](shell_intro/index.html) * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Amanda Charbonneau](https://twitter.com/procrastinomics?lang=en): How to statistics [Slides](https://github.com/ngs-docs/angus/blob/2019/StatsNstuff.pdf) - [view recording](https://www.youtube.com/watch?v=4cndEDLIGVU&feature=youtu.be) * **2:00-2:10pm:** BREAK * **2:15-3:30pm:** [Logging onto the Cloud](jetstream/boot.md) * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** [Conda](conda_tutorial.md) * **5:00pm:** DONE **Thursday, July 4th, 2019** * **9:00-10:20am:** [Quality Control & Adapter Trimming of Sequences](quality-and-trimming.md) * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** [Quality Control & Adapter Trimming of Sequences](quality-and-trimming.md) * **BREAK FOR THE DAY - 4th of July Activities** **Friday, July 5th, 2019** * **9:00-10:20am:** [Finding resources](finding_resources_online.md) * **10:20-10:40am:** BREAK * **10:50am-12:00pm:** [Rayna Harris](https://twitter.com/raynamharris?lang=en) - [RNAseq: a five course meal](https://speakerdeck.com/raynamharris/rnaseq-a-five-course-meal) - [video recording](https://www.youtube.com/watch?v=vAPSd2qPdRI&feature=youtu.be) * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Read Quantification](salmon-quant.md) * **2:00-2:10pm:** BREAK * **2:15-3:30pm:** [Introduction to R & RStudio](R_Intro_Lesson.md) * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** [Introduction to R & RStudio](R_Intro_Lesson.md) * **5:00pm:** DONE ## Second week: July 8-13, 2019. **Monday, July 8th, 2019** * **9:00-10:20am:** [Introduction to R & RStudio cont.](R_Intro_Lesson.md) * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** [Introduction to R & RStudio cont.](R_Intro_Lesson.md) * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Olga Botvinnik](https://twitter.com/olgabot?lang=en) - [Single cell RNAseq (PDF)](https://osf.io/gdzuy/) - [video recording](https://www.youtube.com/watch?v=hAqa8DztxSU&feature=youtu.be) * **2:00-2:10pm:** BREAK * **2:15-3:30pm:** [RNAseq - Differential expression and visualization with R](diff-ex-and-viz.md) * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** [Mapping & Variant Calling](mapping-variant-calling.md) * **5:00pm:** DONE **Tuesday, July 9th, 2019** * **9:00-10:20am:** [Mapping & Variant Calling](mapping-variant-calling.md) and/or [Automation with bash](bash_automation.md) * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** [Automation with bash](bash_automation.md) and/or [Workflow management with Snakemake](snakemake_for_automation.md) * **12:00-1:15pm:** LUNCH * **1:15-2:15pm:** [Shannon Joslin](https://twitter.com/IntrprtngGnmcs?lang=en) - [Genome Assembly](https://osf.io/tnwre/) - [video](https://www.youtube.com/watch?v=P-MunQ9Ew1Y&feature=youtu.be) * **2:15-2:25pm:** BREAK * **2:25-3:30pm:** [Workflow management with Snakemake](snakemake_for_automation.md) (continued) * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** [Adding onto our Snakemake workflow](snakemake_for_qc.md) * **5:00pm:** DONE **Wednesday, July 10th, 2019** * **9a:00-10:20am:** Reviewing [adding onto our Snakemake workflow](snakemake_for_qc.md) * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** [Genome Assembly](de-novo-genome-assembly.md) * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Erich Schwarz](https://twitter.com/ErichMSchwarz?lang=en) - [Doing science with big genomes](https://osf.io/kz5hn/) - [video](https://www.youtube.com/watch?v=xZu6QU63OWQ&feature=youtu.be) * **2:00-2:10pm:** BREAK * **2:15-3:30pm:** [Genome Assembly](de-novo-genome-assembly.md) (continued) * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** Elective Lab: (1) [More Practical Use of Unix](more-unix-fun.md) & (2) BYOD * **5:00pm:** DONE **Thursday, July 11th, 2019** * **9:00-10:20am:** Elective Lab: (1) [Intro to Git](github.md) & (2) BYOD * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** Elective Lab: (1) [Intro to Git](github.md) (continued) & (2) BYOD * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Rocio Martinez-Nunez](https://twitter.com/rociotmartinez?lang=en) - [What comes after ANGUS?](https://osf.io/u4fk5/) * **2:00-2:10pm:** BREAK * **2:15-3:30pm:** Elective Lab: (1) [Microbial Ecology (a discussion on amplicon sequencing and metagenomics)](amplicon_and_metagen.md) & (2) [Transcriptome Assembly](transcriptome-assembly-nematostella.md) and [Annotation](dammit_annotation.md) & (3) BYOD * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** Elective Lab: [Quick Insights from Sequencing Data with Sourmash](sourmash.md) & (2) BYOD * **5:00pm:** DONE **Friday, July 12th, 2019** * **9:00-10:20am:** Elective Lab: (1) [Recovering "genomes" from metagenomes](recovering-rep-genomes-from-mgs.md) & (2) [RNAseq in R](RNA-seq-Analysis.md) & (3) BYOD * **10:20-10:40am:** BREAK * **10:40am-12:00pm:** Elective Lab: (1) [Recovering "genomes" from metagenomes](recovering-rep-genomes-from-mgs.md) (continued) & (2) [RNAseq in R](RNA-seq-Analysis.md) (continued) & (3) BYOD * **12:00-1:00pm:** LUNCH * **1:00-2:00pm:** [Phillip Brooks](https://twitter.com/brooksph?lang=en) - Cloud platforms & Seven Bridges * **2:00-2:10pm:** BREAK * **2:15-3:30pm:** Elective Lab: (1) Seven Bridges & (2) [Overview of Cluster Computing](Intro_to_Cluster.md) & (3) BYOD * **3:30-3:50pm:** BREAK * **3:50-5:00pm:** Elective Lab: (1) Seven Bridges & (2) BYOC (Bring Your Own Cluster\* questions \*for slurm and UGE & (3) BYOD * **5:00pm:** DONE **Saturday, July 13th, 2019** (check out of your rooms and bring luggage over. Please be sure to bring your computer!) * **9:00am-9:30am:** [Cloud Resources](cloud_resources.md) with [Sateesh Peri](https://twitter.com/perisateesh?lang=en) * **9:30am-10:00am:** [5 things I wish I knew](_static/Lee-5-things.pdf) by [Mike Lee](https://twitter.com/AstrobioMike?lang=en) * **10:00am-10:20am:** What to Slack after DIBSI? by [Shannon Joslin](https://twitter.com/IntrprtngGnmcs?lang=en) * **10:20am-10:40am:** BREAK * **10:40am-11:00am:** Survey in Room 1030 * **11:00am-11:30am:** Classroom feedback--1up/1down (in classrooms) & TA / Instructor meeting (in Rm1030) * **11:30am-12:00pm:** Titus Wrap up & Outro * **12:00pm:** THANK YOU & HAPPY TRAVELS! [Some contact info](feel-free-to-reach-out.md) 😊