Linux Basics For NGS Data Analysis

DNA and computer illustration

2022 dates(s):

On-Line:
Monday, February 21 – 9am – 4pm

In person:
Monday, June 13 – 9am – 4pm

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

REGISTER from calendar on Workshop page.

It is necessary to register for each workshop separately.

Linux Basics For NGS Data Analysis


Description

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 inquire 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 fee ( $95)  is required for each student.

* 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.