KNVM Division Microbial Typing: Data Carpentry Genomics

25-26 november 2019

9.00 to 17.00

Instructors: Anita Schürch, Sergio Arredondo Alonso, Sam Nooij, Dennis Schmitz

Helpers: Duong Vu, Jorge Navarro, Mattias de Hollander, Barbara Vreede

General Information

This is a Data Carpentry Genomics workshop with a special focus on handling and analysing microbial genomics data. This workshop teaches the fundamental data skills needed to conduct research. Its target audience are researchers who have little to no prior computational experience. The lessons build on learners' existing microbial 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".

Who: The course is aimed at graduate students and other researchers, with a background in microbiology. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: BCN Utrecht, Daltonlaan 100, 3584BJ Utrecht. Get directions with OpenStreetMap or Google Maps.

When: 25-26 november 2019. Add to your Google Calendar.

Costs: The registration costs are 175 Euro and include coffee/tea, lunch and drinks at the end of the workshop.

Registration: Register here.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (Spreadsheet program, putty) for which installation instructions are indicated here..

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

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 or for more information.


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

Pre-workshop Survey

Post-workshop Survey


Day 1

Before starting Pre-workshop survey
9.00 Project Organization and ManagementDennis
10.30 Break
10.45 Introduction to the Command LineSam
13.15 Lunch
14.00 Intro to the Command Line continuedSam
15.00 Data Wrangling and ProcessingDennis
17.00 END

Day 2

9.00 Data Wrangling and Processing continuedAnita
10.30 Break
12.30 Introduction to Cloud Computing for GenomicsAnita
13.15 Lunch
14.00 Intro to R and Rstudio for GenomicsSergio
16.55 Post-workshop survey
17.00 Drinks

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