Bioinformatics basics for trainee students
October 4, 2023 · View on GitHub
This GitHub was originally intended to introduce trainee students of the EVO • COM group of the University of Bologna to the Bash environment. However, this GitHub is obviously freely available for use by anyone who may find it helpful.
Here you will find a friendly resource for accessing commonly used commands in early bioiformatics.
🪅 Enjoy!
What's inside this repository?
Very few files, actually, but fairly packed. Commands and explanations are presented in markdown files and are divided into macro-topics. They are numbered in the order I tipically use for teaching students. A series of example files are also provided.
| Macro-topic | Description |
|---|---|
| 01 - Bash basics | The very first introduction to bioinformatics. Look here for basic bash commands and operations. |
| 02 - Working with Conda | What's Conda and how to use it. |
| 03 - Working with screen sessions | What's a screen session and how to use it. |
| 04 - git and GitHub | What's git and how to use it. |
Example files/ | A directory containing several files used to test commands. |
download_PDFs/ | A directory containing the PDF version of markdown files to be downloaded |
Useful textbooks and other resources
- 📚 Unix in a nutshell by Arnold Robbins (2005), O'Reilly Media, Inc.
- 📚 Bioinformatics data skills by Vince Buffalo (2015), O'Reilly Media, Inc.
- 📚 Bash scripting cheatsheet by Rico Sta. Cruz.
- 📝 Notes by Mariangela Iannello (bash basics, scripting, transcriptome assembly/annotation pipelines, and gene differential expression) and notes by Jacopo Martelossi (bash basics, scripting, genome assembly and annotation, orthology inference)!!