NOTE: This list will be constantly updated.
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Bioinformatics workshop platform: https://bioinformaticsworkbook.org/
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Programming for Biology 2019 (CSH) http://programmingforbiology.org/index.html
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Software Carpentry: The Unix Shell: http://swcarpentry.github.io/shell-novice/
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Software Carpentry: Other lessons: https://software-carpentry.org/lessons/index.html
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The Linux Documentation Project (TLDP): https://www.tldp.org/guides.html
- Bash Guide for Beginners: The Bash Guide for Beginners gets you started with Bash scripting and bridges the gap between the Bash HOWTO and the Advanced Bash Scripting Guide. Everybody who wants to make life easier on themselves, power users and sysadmins alike, can benefit from reading this practical course. The guide contains lots of examples and exercises at the end of each chapter, demonstrating the theory and helping you practice. Bash is available on a wide variety of UNIX, Linux, MS Windows and other systems.
- Introduction to Linux: A Hands on Guide: This guide was created as an overview of the Linux Operating System, geared toward new users as an exploration tour and getting started guide, with exercises at the end of each chapter. For more advanced trainees it can be a desktop reference, and a collection of the base knowledge needed to proceed with system and network administration. This book contains many real life examples derived from the author's experience as a Linux system and network administrator, trainer and consultant. We hope these examples will help you to get a better understanding of the Linux system and that you feel encouraged to try out things on your own.
- GNU/Linux Command-Line Tools Summary: This document is an attempt to provide a summary of useful command-line tools available to a GNU/Linux based operating system, the tools listed are designed to benefit the majority of users and have being chosen at the authors discretion. This document is not a comprehensive list of every existent tool available to a GNU/Linux based system, nor does it have in-depth explanations of how things work. It is a summary which can be used to learn about and how to use many of the tools available to a GNU/Linux-based operating system.
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Version control
- git [EBOOK] Pro Git by Scott Cachon and Ben Straub
- git(1) Manual page
- git documentation
- Atlassian - Learn Git with Bitbucket Cloud
- Tower - Learning Version Control with Git
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Clusters
- Lecture on clusters open access here
- Software carpentry: Introduction to high=performance computing
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Applied computational genomics lecture by Aaron Quinlan (Univ. Utah)
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Hummingbird resources:
- Tutorials and documentation available on the Hummingbird's website
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Python:
- List of Python tutorials and resources from Python.org
- Google for Education > Python
- Software carpentry: Python fundamentals
- Automate the Boring Stuff with Python - Practical Programming for Total Beginners by Al Sweigart BOOK
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Introduction to genomic analyses: This course is intended for Canadian researchers interested in learning the basic steps of genomic analysis using high performance computing. Using the computing resources of Compute Canada, specifically the WestGrid region, participants will work through practical exercises in the workshop sessions and receive a certificate of completion at the end of the series.