Linux Essentials for Next-Generation Sequencing Data Analysis

Note: required before taking any other workshop. Check dates. (Statement of proficiency in bash shell accepted.)

2017 Fall/Winter dates: 


September 13- 9am - 4pm
October 04  - 9am - 4pm

November 01  - 9am - 4pm
December 01 - 9am - 4pm


LocationGenetics/Biotech Center
425 Henry Mall Madison, WI 53706

LIMITED to 10 participants - (4 minimum)

REGISTER: use Google Calendar link on chosen date to register (opens in new TAB or new window.)

This workshop is aimed at researchers interested in using open source tools for analyzing Next Generation DNA Sequencing (NGS) data.

Students will learn the essential techniques to interact with the powerful Linux operating system via the bash shell commands that are necessary to leverage the capabilities of many of the latest most popular bioinformatics tools used in NGS analysis. A central goal of the workshop is to make users more comfortable with what is likely an unfamiliar computing environment so that they can more confidently understand and employ these methods in the context of their independent research projects. 

This workshop is a preparation to all other workshops and provides insights to essential Linux commands, and for most applicants is a required session. (Statement of proficiency might be acceptable - enquire by email)

The workshop consists of lecture material with emphasis on active hands-on exercises.

Materials will cover the following topics:

  • Edit text files and scripts
  • Copy, remove and unzip files
  • Find patterns
  • Navigate directories
  • Set environment variables
  • rapid overview of simple NGS pipeline

The computer laboratory exercises require that students bring a laptop* to connect to the Linux system in the Biotechnology Center.  

A $95 fee is required for each student and includes costs for a printed manual workbook of about 115 pages or more.

* There is a minimal set of software that should be installed on laptops BEFORE attending the workshop. Instructions will be provided to attendees prior to the workshop and can be found within the PDF document: GETTING PREPARED FOR CLASS (Opens in new TAB or new window.)

Instructor(s):
Dr. Jean-Yves Sgro,  Ph.D., Biotechnology Center - jsgro@wisc.edu

Previous instructor(s):
Dr. Deborah Muganda-Rippchen, Ph.D. Center for Predictive Computational Phenotyping
Dr. Jeremy Glasner, Ph.D.,  Biotechnology Center

*No-show Policy*
All cancellation need to be notified 72 hours in advance.