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Genome Assembly Workshop Part I: Project Design, Sequencing Technologies and Library Methods (9/25/2017)
When and where
Date and time
Location
Koshland Hall 238 Berkeley, CA 94720
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Description
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.