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      Introduction to the Command Line for Bioinformatics

Introduction to the Workshop and the Core
Cheat Sheets
Introduction to the Command Line 1
Introduction to the Command Line 2
Introduction to the Command Line 3
High Performance Computing
Closing thoughts
Github page
Biocore website

Quick Introduction to the Workshop and Core

The mission of the Bioinformatics Core facility is to facilitate outstanding omics-scale research through these activities:


Staff and Students

Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when appropriate, and/or develop novel applications and pipelines when needed, however we always emphasize biological interpretation of the data.



Structure of the Virtual Workshops

Given the current Covid19 pandemic, and stay in place orders around the world, we’ve decided to take our popular bioinformatic workshops virtual. Our intent is to offer as close to an experience we can to our in-person workshops. We will hold the same goals and strive for a similar lecture/hand-on ratio. We will be using multiple technologies in order to help facilitate a maximum amount of interaction.


Course lecture, discussions, and one-on-one help/troubleshooting will be conducted using a zoom meeting.

Because video is involved, we ask everyone to be respectful and we reserve the right to remove someone if they are being disrespectful or disruptive.

Learn more about how we use Zoom in our workshops.


Text based communication will be conducted via a Slack channel. Staff will be monitoring the Slack channel to answer questions (and schedule a Zoom break out room if needed). If you know the answer to someone else’s question, feel free to answer it.

Learn more about how we use Slack in our workshops.


We ask for a little more patience as this process is also new to us, but we are committed to providing you the best educational experience we can (under the current conditions).

Workshop Goals

This workshop is intended to provide a comprehensive introduction to the basics of the command line as it is used for bioinformatics. By the end of the third session, participants should:

Workshop Materials

Workshop materials are all posted on github, and publicly available


Computing Cluster

A portion of this course will be conducted on our servers and compute cluster (tadpole.genomecenter.ucdavis.edu).

Everyone should get an account.

Request an account -> sponsor is “Bioinformatics Core Workshop”

If you already have, or have had in the past, an account on our systems, then please tell us your username, or email, and we will add you to the workshop. Do not create a new account