A Quick Guide to Getting Started with Shell and BLAST

Written by Jia Liu, Paul Villanueva, and Adina Howe.

This is material for a workshop hosted on 11/17/2020 by the GERMS lab. The goal of the workshop is to get someone with no experience with the command line completing doing basic BLAST commands in a few hours.

In order to complete this workshop, you’ll need:

1. A shell client. If you’re using a Mac, you can use the built-in Terminal program. If you’re using Windows, you’ll need to download a program like Gitbash or PuTTY.

2. The materials for the workshop. The materials for the workshop are available at the Github repo. You can download them to your computer by typing git clone https://github.com/germs-lab/blast_crash_course.git in your shell program.

Note

If you’re attending the workshop on 11/17/2020 by VI Escuela Regional de Microbiología, you will have a different set up for this and there is no need for you to follow these directions.

Contents:

• 1. File Navigation and Listing
  • 1.1. Where are we? And what’s in here?
• 2. Working with files
  • 2.1. Counting, listing, and using *
  • 2.2. Creating, writing to, and deleting files
  • 2.3. Copying, removing, and renaming files
  • 2.4. Using * to combine files
  • 2.5. Creating and deleting directories
• 3. Searching files with GREP
  • 3.1. Basic grep searches
  • 3.2. Using grep with fasta files
• 4. Introduction of BLAST
  • 4.1. Authored by: Jia Liu, Paul Villanueva, and Adina Howe; MODIFIED from a previous tutorial
• 5. Section 1. Learning objectives
  • 5.1. Objectives
  • 5.2. Pre-requisites
  • 5.3. Mission
• 6. Section 2. Set up BLAST
  • 6.1. What is BLAST?
  • 6.2. Preparation
  • 6.3. Download BLAST
  • 6.4. Install BLAST
• 7. Section 3. BLAST Analysis
  • 7.1. Overview
  • 7.2. Project 1. Understand BLAST with small datasets
  • 7.3. Project 2. Apply BLAST on real datasets
• 8. Conclusion

Acknowledgement:

This work was supported by the National Science Foundation Directorate of Biological Sciences under awards DEB 1737758 and DEB 1737765.