Basic sequence manipulation

(Gabor Marth)

Introduction

The purpose of this session is to learn some of the basic steps of sequencing informatics and analysis. Equally importantly, you will learn how to automate analysis by stringing together subsequent steps of the process. In other words, you will write a sequence processing pipeline, a simple version of what is currently en vougue at sequencing centers today.

During the lecture, we will go through sequence assembly step by step, manually executing programs to perform base calling, vector clipping, sequence assembly, and some post-assembly analysis: oligo selection and repeat masking. During the practical session, we will concentrate on developing the automated assembly pipeline. Finally, in the homework assignment, you will be asked to write programs that should expand your skills in software-aided sequence handling.