Assignment of Function and Taxonomy to Metagenomic Reads using the GORG-classifier

For this lesson, we are going to work with output data from the GORG-classifier. The GORG-classifier uses Kaiju to compare metagenomic reads to high quality genomes from GORG-Tropics to provide functional and taxonomic annotations to each individual read. If you want to install and run the GORG-classifier on your own, you can find installation instructions on its github page.

For the purpose of today's lesson, we've run the GORG-classifier for you on some pet metagenomes from BATS. See GORG-classifier_setup.ipynb for details.

Setup your lesson environment

If you haven't already, let's create a directory for this lesson in your user lab.

In terminal, navigate over to your user lab directory and clone the lesson repository.

$ cd ~/storage/user_lab/{your_username_here}/
$ git clone https://github.com/Bigelow-SCG-Course/Day3PM_GORG-classifier.git

You should now have a directory called '3PM_GORG-classifier' within your user directory.