This repository contains a tutorial on how to use command-line genomics/bioinformatics tools in Linux. It has been designed for BIOL 469 (Genomics) and BIOL 614 (Bioinformatics Tools and Techniques) @ the University of Waterloo.

It is divided into a series of tasks

• Task 1 - Learning the linux command line
• Task 1b - Command-line BLAST
• Task 2 - Genome Assembly
• Task 3 - Genome Annotation
• Task 4 - Comparative genomics: synteny comparison genomes
• Task 5 - Comparative genomics: gene set comparison between two genomes
• Task 6 - Resequencing: variant calling from NGS data
• Task 7 - Transcriptomics and detection of differentially expressed genes
• Task 8 - 16S rRNA amplicon sequencing analysis using Kraken2+Bracken
• TBD - ChIP-seq data analysis
• TBD - GWAS
• TBD - Metagenomics: taxonomic and functional profiling

The main requirement is that you have access to a Linux-based OS such as Ubuntu. If you have access through a remote server that has been supplied to you, then you are set. If not, then one option is to install a Linux VM as a Virtual Machine on your local system, or use the Google Compute Engine (e.g., free credits) ).

Most of the programs we will use are text-based and can be run directly in the shell; however, some graphical programs (e.g., Tablet, Artemis, fastqc) will be used as well. You can install these on your own local machine.

Detailed software requirements will be listed at the beginning of each Task. Alternatively, if you wish to install all the programs for the course beforehand, please install the software listed below:

• tablet
• artemis and act
• bandage
• R

We have also documented installation instructions for building a bioinformatics system (Ubuntu 18.04) here.

If you have any questions, please contact acdoxey at uwaterloo dot ca.

Enjoy