Data Carpentry Genomics Workshop - George Washington University

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 or Google Maps.

HOW TO APPLY: Click on this link 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:



ACCESSIBILITY: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

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.




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

10:15-11:00am : Introduction to CyVerse Atmosphere Cloud

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

11:15-12:30pm : BASH - Command Line for Genomics

12:30-1:30pm : Lunch Break

01:30-3:00pm : BASH - Continued & Bioconda

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

03:30-4:30pm : Overview of Genomics Analysis Workflow

04:30-5:30pm : Assessing Read Quality


09:30-10:15am : Trimming and Filtering

10:15-11:00am : Variant Calling Workflow

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

11:15-12:30pm : Automating the workflow using shell scripts

12:30-01:30pm : Lunch Break

01:30-04:30pm : Building Reproducible Workflows with Snakemake

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

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

Notepad for the workshop : Click here


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

Data Carpentry (part of The Carpentries) 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”.