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Welcome to your DIB-lab rotation project! All resources needed to learn a metagenomics workflow are contained within this repository. If you see a mistake or something is not clear, please submit an issue.

During this rotation, you will learn how to:

• interact with an HPC (we'll use Farm)
• install and manage software environments using conda
• download sequencing data and other files from the internet and public databases
• interpret and use different file formats in bioinformatics and computing
• quality analysis and control for sequencing data
• determine the taxonomic composition of sequencing reads
• assemble and annotate metagenomic reads
• quickly compare large sequencing datasets
• document workflows using git and GitHub.

The files in this repository are ordered by execution, meaning file 00* should be completed before 01*.

Most of the work done in this rotation will be completed on Farm. However, you will need to access Farm from your own computer. We will use an SSH-client to be able to interact with Farm. If you are using a Mac or a Linux, your computer comes with a program called Terminal that we will use as an SSH-client. If you are on a Windows running Windows 10, you can install the Ubuntu Subsystem. Otherwise, please follow the instructions for Windows found at this link. You can also look at workshops 3 and 4 in our Introduction to Remote Computing.