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# **Data Carpentry Genomics Workshop - George Washington University**

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**WHEN:** **April 11-12, 2019 (9:30 AM - 5:30 PM)**

**WHERE:** **Gelman Library, 2130 H St NW, Room 301/302, Washington, DC 20052** . Get directions with [OpenStreetMap](https://osm.org/go/ZZcbJto48?way=66409261) or [Google Maps](https://goo.gl/maps/vZdYWxLsZwQ2).

**HOW TO APPLY:** Click on this [**link**](https://www.eventbrite.com/e/george-washington-university-data-carpentry-workshop-tickets-58597869806) to register for the workshop.

**TARGET AUDIENCE:** **Students, Researchers & Faculty**
> Little to no prior computational experience required.
> > The instructors will prioritize creating a friendly environment that will empower researchers and enable data-driven discovery. Even those with some experience will benefit, as the goal is to teach not only how to do analyses, but how to manage the process to make it as automated and reproducible as possible.

**Learning objectives for this workshop:**
+ Accessing Cloud Computing Resources
+ UNIX command line
+ Environment management using Conda & Bioconda
+ Building Reproducible Workflows


**REQUIREMENTS:**
- Laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) and administrative privileges.
  > No prior-software installation required. Windows users can install [mobaxterm](http://mobaxterm.mobatek.net/download-home-edition.html) for a UNIX terminal.

- Register for a free account on CyVerse [**Here**](https://user.cyverse.org/workshops/30/overview)

- Complete [**Pre-Workshop survey**](https://www.surveymonkey.com/r/dcpreworkshopassessment?workshop_id=2019-04-11-gwu). *We use this to calibrate the pace of the workshop and, together with a post-workshop survey, to assess how it went.*

**CODE OF CONDUCT:**
- The workshop follows a code of conduct, which can be found [here](https://gwu-omics2019.readthedocs.io/en/latest/code_of_conduct.html). (*tl;dr:* Be Nice and Respect each other.)

**ACCESSIBILITY:** We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
  + The room is wheelchair / scooter accessible.
  +  Accessible & Gender-Neutral restrooms are available.

> Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

**CONTACT:** Please email **Megan Potterbusch** at (mpotterbusch@email.gwu.edu) for more information.

**INSTRUCTORS**
* **Niel Infante**
  + Twitter - (https://twitter.com/Niel_Infante)
  + Email: (aminfante@hsc.wvu.edu)
* **Sateesh Peri**
  + Twitter - (https://twitter.com/perisateesh)
  + Email: (perisateesh@nevada.unr.edu)

  **HELPERS**
  * **Adam Wong** - (aklwong@gwu.edu)
  * **Keylie Gibson** - (kmgibson@gwmail.gwu.edu)
  * **Rebecca Clement** - (rebeccaclement@gwmail.gwu.edu)
  * **William Bonnett** - (synchronous@email.gwu.edu)


**SCHEDULE**

**Day-1**

09:30-10:15am : Introduction and Genomics Workshop Overview

10:15-11:00am : [Introduction to CyVerse Atmosphere Cloud](https://gwu-omics2019.readthedocs.io/en/latest/atmosphere_cloud.html)

11:00-11:15am : Coffee/Tea break

11:15-12:30pm : [BASH - Command Line for Genomics](https://gwu-omics2019.readthedocs.io/en/latest/bash_lesson_1.html)

12:30-1:30pm  : Lunch Break

01:30-3:00pm  : [BASH - Continued](https://gwu-omics2019.readthedocs.io/en/latest/bash_lesson_2.html) & [Bioconda](https://gwu-omics2019.readthedocs.io/en/latest/bioconda_lesson.html)

03:00-3:30pm  : Coffee/Tea Break

03:30-4:30pm  : [Overview of Genomics Analysis Workflow](https://gwu-omics2019.readthedocs.io/en/latest/workflow_overview.html)

04:30-5:30pm  : [Assessing Read Quality](https://gwu-omics2019.readthedocs.io/en/latest/quality_control.html)

**Day-2**

09:30-10:15am : [Trimming and Filtering](https://gwu-omics2019.readthedocs.io/en/latest/trimming.html)

10:15-11:00am : [Variant Calling Workflow](https://gwu-omics2019.readthedocs.io/en/latest/variant_calling.html)

11:00-11:15am : Coffee/Tea break

11:15-12:30pm : [Automating the workflow using shell scripts](https://gwu-omics2019.readthedocs.io/en/latest/automation.html)

12:30-01:30pm : Lunch Break

01:30-04:30pm : [Building Reproducible Workflows with Snakemake](https://gwu-omics2019.readthedocs.io/en/latest/snakemake_basic.html)

02:30-03:00pm : Coffee/Tea Break

04:30-05:30pm : Discussion & End of workshop

> Notepad for the workshop : Click [here](https://hackmd.io/nPo6cXDOSye5I0tOqeF3Jg#)

**SURVEYS**

Please click on the links below to complete the surveys before and after the workshop.

- Click [here](https://www.surveymonkey.com/r/dcpreworkshopassessment?workshop_id=2019-04-11-gwu) to answer the Pre-Workshop survey.

- Click [here](https://www.surveymonkey.com/r/dcpostworkshopassessment?workshop_id=2019-04-11-gwu) to answer the Post-Workshop survey.

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![](/img/carpentries_logo.png)

[**Data Carpentry**](https://datacarpentry.org/) (part of [The Carpentries](https://carpentries.org/)) develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. For more information on what we teach and why, please see our paper "[Good Enough Practices for Scientific Computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)".