Assignment 1

This is a test to make sure that you have the AWS image up and running and that you can access it and generate meaningful results.

It will also familiarize you with NCBI EDirect that we will use during the course.

The file genera.txt is a plain text file that you can read on the command line using less or more. The file has 69 different organisms, listed as genus and species, with one entry per line. The assignment is to familiarize yourself with NCBIs EDirect tool and to use some advanced bash scripting.

In the first part of the assignment, you must identify which organism has the most number of genomes in the assembly database. You should use on of the edirect scripts provided on the AWS image to complete that task as shown in the manual.

In the second part of the assignment, you must calculate the AVERAGE (mean) genome size of the genomes associated with “Prevotella buccalis”.

Hint: There is a command called countfasta.py that will likely help you with this step!