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University of Wisconsin–Madison

Bioinformatics Resource Center

The UW-Madison Biotechnology Center is currently open and following the university's COVID-19 Response regarding campus operations.

Linux Essentials for Next-Generation Sequencing Data Analysis

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


2021 On-Line dates(s): 

Monday, April 05 - 9am - 4pm
Monday, July 12 - 9am - 4pm 

Location: During Covid-19: Online (WebEx or other)
Genetics/Biotech Center
425 Henry Mall Madison, WI 53706

LIMITED to 12 participants - (2 minimum)

REGISTER: use Google Calendar link on chosen date to register (opens in new TAB or new window.)
NOTES: 
It is necessary to register for each workshop separately.
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Printed original exercise bookif registration is less than 1 week a photocopy version may be substituted. ((Noteduring COVID19 - book provided as PDF)

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 of bash may be acceptable - please enquire by email.)

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

Materials will cover the following topics:

  • Remote connection to a linux server
  • Edit text files and scripts
  • Copy, remove and unzip files
  • Find patterns
  • Explore the power of input/output standards with "pipes" and "redirection"
  • Create and 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 ($75 online during COVID19)  is required for each student and includes costs for a printed manual workbook of about 115 pages or more. (Noteduring COVID19 - book provided as PDF)

* 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: Preparation for Linux-based workshop  (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 cancellations need to be notified 72 hours in advance.