2021 On-Line dates(s):
Monday, April 05 – 9am – 4pm
Monday, July 12 – 9am – 4pm
Monday, September 20 – 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.
– Printed original exercise book: if registration is less than 1 week a photocopy version may be substituted. ((Note: during COVID19 – book provided as PDF.)
Linux Basics For NGS Data Analysis
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 $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. (Note: during 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.)
Dr. Jean-Yves Sgro, Ph.D., Biotechnology Center – email@example.com
Dr. Deborah Muganda-Rippchen, Ph.D. Center for Predictive Computational Phenotyping
Dr. Jeremy Glasner, Ph.D., Biotechnology Center
All cancellations need to be notified 72 hours in advance.