Wed, Oct 9, 2013 - Illumina; shotgun sequencing; read QC

Outline of day:

1. Technical challenges of homework; long-running jobs

Review: starting up machines; connecting with SSH or IPython Notebook.

Copy/paste and putting in complete commands.


Long running jobs; using screen.


Shell vs IPython Notebook.

(I will deliver videos of all of these tonight.)

2. Shotgun sequencing with Illumina

(To follow along with lecture go to and enter ‘titus’.)

How Illumina works.

Assumptions underlying shotgun sequencing.

How the data is delivered.

3. Quality scores, and quality evaluation

Discuss some FastQC results here:

and here:

What other ways might there be to evaluate the quality of your sequencing data? (Think about things you already know, or can assume...?)

4. What do you do with sequencing data?

Mapping vs assembly. (This will be a continuing theme :)

5. Homework solutions

See: solutions.

6. More Python

Last week was “control flow” – for and if. This week, “data structures” – ways of storing aggregate information.

See: in-class notebook.