1. Next-Gen Sequence Analysis Workshop (2019)¶

These are the schedule and classroom materials for the ANGUS workshop at UC Davis, which will run from July 1st to July 13th, 2019. ANGUS is part of the 2019 Data Intensive Biology Summer Institute.

This workshop runs under a Code of Conduct. Please respect it and be excellent to each other!

We hope that we can respect each other by following these guidelines & expectations.

Please submit your feedback here on any aspect of the workshop. We encourage feedback from everyone involved in the workshop in any capacity

Twitter hash tag: #dibsi2019

1.1. 3 Rooms & lead instructors!¶

Room Mexía will be led by Rocio Martinez-Nunez and Taylor Reiter, in 1043 Valley.

Room Lovelace will enjoy the leadership of Chissa Rivaldi and Mike Lee, in 1041 Valley.

Room Conway will be led by Sateesh Peri & Marian Schmidt, in 2020 Valley.

Monday, July 1st, 2019:

1:30-2:20pm: Welcome to ANGUS 2019 slides
- 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
- 5:00pm: DONE

Tuesday, July 2nd, 2019:

9:00-10:20am: Introduction to the Shell
- 10:20-10:40am: BREAK
10:40am-12:00pm: Introduction to the Shell
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Lisa K Johnson: Intro to Modern Sequencing Practices - view recording!
- 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
- 10:20-10:40am: BREAK
10:40am-12:00pm: Wrapping up Introduction to the Shell
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Amanda Charbonneau: How to statistics Slides - view recording
- 2:00-2:10pm: BREAK
2:15-3:30pm: Logging onto the Cloud
- 3:30-3:50pm: BREAK
3:50-5:00pm: Conda
- 5:00pm: DONE

Thursday, July 4th, 2019

9:00-10:20am: Quality Control & Adapter Trimming of Sequences
- 10:20-10:40am: BREAK
10:40am-12:00pm: Quality Control & Adapter Trimming of Sequences
- BREAK FOR THE DAY - 4th of July Activities

Friday, July 5th, 2019

9:00-10:20am: Finding resources
- 10:20-10:40am: BREAK
10:50am-12:00pm: Rayna Harris - RNAseq: a five course meal - video recording
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Read Quantification
- 2:00-2:10pm: BREAK
2:15-3:30pm: Introduction to R & RStudio
- 3:30-3:50pm: BREAK
3:50-5:00pm: Introduction to R & RStudio
- 5:00pm: DONE

Monday, July 8th, 2019

9:00-10:20am: Introduction to R & RStudio cont.
- 10:20-10:40am: BREAK
10:40am-12:00pm: Introduction to R & RStudio cont.
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Olga Botvinnik - Single cell RNAseq (PDF) - video recording
- 2:00-2:10pm: BREAK
2:15-3:30pm: RNAseq - Differential expression and visualization with R
- 3:30-3:50pm: BREAK
3:50-5:00pm: Mapping & Variant Calling
- 5:00pm: DONE

Tuesday, July 9th, 2019

9:00-10:20am: Mapping & Variant Calling and/or Automation with bash
- 10:20-10:40am: BREAK
10:40am-12:00pm: Automation with bash and/or Workflow management with Snakemake
- 12:00-1:15pm: LUNCH
1:15-2:15pm: Shannon Joslin - Genome Assembly - video
- 2:15-2:25pm: BREAK
2:25-3:30pm: Workflow management with Snakemake (continued)
- 3:30-3:50pm: BREAK
3:50-5:00pm: Adding onto our Snakemake workflow
- 5:00pm: DONE

Wednesday, July 10th, 2019

9a:00-10:20am: Reviewing adding onto our Snakemake workflow
- 10:20-10:40am: BREAK
10:40am-12:00pm: Genome Assembly
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Erich Schwarz - Doing science with big genomes - video
- 2:00-2:10pm: BREAK
2:15-3:30pm: Genome Assembly (continued)
- 3:30-3:50pm: BREAK
3:50-5:00pm: Elective Lab: (1) More Practical Use of Unix & (2) BYOD
- 5:00pm: DONE

Thursday, July 11th, 2019

9:00-10:20am: Elective Lab: (1) Intro to Git & (2) BYOD
- 10:20-10:40am: BREAK
10:40am-12:00pm: Elective Lab: (1) Intro to Git (continued) & (2) BYOD
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Rocio Martinez-Nunez - What comes after ANGUS?
- 2:00-2:10pm: BREAK
2:15-3:30pm: Elective Lab: (1) Microbial Ecology (a discussion on amplicon sequencing and metagenomics) & (2) Transcriptome Assembly and Annotation & (3) BYOD
- 3:30-3:50pm: BREAK
3:50-5:00pm: Elective Lab: Quick Insights from Sequencing Data with Sourmash & (2) BYOD
- 5:00pm: DONE

Friday, July 12th, 2019

9:00-10:20am: Elective Lab: (1) Recovering “genomes” from metagenomes & (2) RNAseq in R & (3) BYOD
- 10:20-10:40am: BREAK
10:40am-12:00pm: Elective Lab: (1) Recovering “genomes” from metagenomes (continued) & (2) RNAseq in R (continued) & (3) BYOD
- 12:00-1:00pm: LUNCH
1:00-2:00pm: Phillip Brooks - Cloud platforms & Seven Bridges
- 2:00-2:10pm: BREAK
2:15-3:30pm: Elective Lab: (1) Seven Bridges & (2) Overview of Cluster Computing & (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 with Sateesh Peri
9:30am-10:00am: 5 things I wish I knew by Mike Lee
10:00am-10:20am: What to Slack after DIBSI? by Shannon Joslin
- 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!