Principles and Applications of Modern DNA Sequencing


Session 2: Intro to Genomics and Python

Notebook 1.2: Genome Databases

FTP allows you to access a file system through your browser.

The refseq/ directory contains genomes that are annotated, meaning they contain files with information about where genes, and other genomic features (e.g., telomeres) are located. While we of course hope to learn what all of these features are, you don't need to know yet. They are simply labeled things in the genome that are marked with a start and stop position.

Link to FTP

Assigned reading

Assigned reading

Sanger sequencing technology

Illumina sequencing technology

Nanopore sequencing technology

Why Python?

Is it fast enough?

Why Python?

Easy to use, readable, extendable (e.g., C/C++ bindings), mature. Python is often the glue that binds programs/code/web.

Python tutorials

Python has been around for 20 years, and so there are many resources for learning Python online. For extra help I recommend looking for *modern* tutorials. That means tutorials that use IPython/jupyter, and which teach Python3 as opposed to Python2.

The tutorials we have selected, and created, aim for modern Python use.

Getting started with Python

Learn by doing. Run the pre-written code in the assignment notebooks, modify it, see how it changes, learn from it. *Try* to solve the assigned problems on your own before you seek help.

Search for answers when you are stuck. If you get an error, type that error into google to learn what it means. If you want to learn how to create a list of list objects in python, google "python create a list of lists"

Don't stress out. You can't learn programming all at once, it takes time and *practice*. You'll pick it up through repetition, reading code, and *trying* to solve problems with code. That is the purpose of our exercises.

Interactive Python (it's here to help you)

Take advantage of the *interactive* nature of Python in jupyter. Use [tab]-completion to view attributes/functions of objects, and use shift+tab to view documentation notes for functions.


Complete Unit 2 on Codio: 4 notebooks.

Read chapters 1,3,4,5,6,7 of The official Python tutorial