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A Data Carpentry Workshop

The Donald Danforth Plant Science Center

June 17, 2017

9:00 am - 5:00 pm

Instructors: Bo Ji, Catalina Anghel

Helpers: Alex Harkess, Patricia Baldrich

General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.

Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Who: The course is aimed at graduate students and other researchers.

Where: Mary and Oliver Langenberg Theater, 975 North Warson Road, St. Louis, MO. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.


We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Morning: 9:00AM - 12:00PM

Module 1: Data and project organization
Intro to Data Carpentry Bo
Intro to Data and Genomics Data Tidiness (brief overview) Bo
Module 2: Using cloud computing for genomics
  • understand what cloud computing is and why it's useful
  • log in to remote computing resources
Connecting to the Cloud in 5 Minutes or Less Bo
Module 3: Introduction to the command line
Using the Command Line (Shell) Bo (a short introduction by Catalina)

Afternoon: 1PM - 5:00PM

Module 3, continued (if needed): Command line
Using the Command Line (Shell) Catalina
Module 4: Running bioinformatics programs and creating workflows
  • Quality control of NGS Data
  • Automating a workflow
QC of Sequence Data Catalina
Automating Workflows (up until the shell script) Catalina

Post Workshop

Alignment and Variant Calling
Automating Workflows On Your Own
Variant Calling On Your Own
How To Make This Work Your Own
Launching Your Own Cloud Instances On Your Own


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Please follow these Setup Instructions.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.