Genome Assembly Workshop Part I: Project Design, Sequencing Technologies and Library Methods (9/25/2017)

Workshop Outline:

Sept. 25, 2017

Basics and A Priori Knowledge of the Genome to be Sequenced

Prior knowledge about the genome that will be sequenced can help in choosing the appropriate sequencing and assembly strategy. Here, I will cover some basics and then discuss different genome characteristics that strongly influence whether a genome will be easy or difficult to sequence and assemble successfully.

Sequencing Platforms

I will outline different 1st, 2nd and 3rd generation sequencing strategies. The sequencing platforms I will cover in this section include Illumina (MiSeq and HiSeq), IonTorrent, IonProton, ABI Solid, PacBio, Nanopore and Helicos.

Sequencing Library Setup

I will discuss the differences (including pros and cons) of Illumina library preparation methods, such as paired-end (PE), mate pair (MP), TrueSeq Synthetic Long-Reads and 10X genomics Linked Long-Reads. In this section, I will also outline other strategies such as BAC or fosmid based sequencing and chromosome folding based long-range linkage methods such as Dovetail Genomics’ Chicago library.