Genome Assembly Workshop

Short-course: Genome Assembly for Biologists

Tentative schedule, please check back as we refine our workshop content

Day 1

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, ABI Solid, PacBio, Nanopore and the BGIseq-500.

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) and 10X genomics Linked Long-Reads. 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 and different HiC library methods.

Day 2

Raw Read Data Processing

In this section, I will talk about tools used to assess, as well as, improve sequencing read quality.

De-Novo Assembly Strategies and Tools

To make the workshop more useful, I will outline the different popular assembly tools (for assembly of large genomes) and briefly discuss the underlying algorithms. By doing so, I will also explain terms commonly used in genome assembly  ( e.g. kmer, N50, etc).

Assembly Quality Assessment

A critical step after assembling a genome is assessing the quality of the resulting sequence. In cases where different assemblers or different kmer sizes are used, tools are needed to decide which of the assemblies is the best.

Bioinformatic Assembly Improvement

There are different tools that can be used to improve the genome sequence after the initial assembly, either by filling gap regions or finding and resolving mis-assembled regions. Furthermore, genome assemblies can be merged to improve quality.

Lab-based Assembly Improvement

In this section, I will briefly discuss the pros and cons of Physical and Optical Mapping methods (such as BioNano’s Iryis platform).

Draft vs. Finished Assembly

A crucial decision in genomics is whether a genome assembly is good enough to address the desired research questions. Here, I will explain the differences between finished and draft genome assemblies, and give some guidance on deciding if further sequencing is needed or not.

Downstream Analyses

To conclude the workshop, I will briefly outline subsequent downstream processing and analyses steps, such as repeat and gene annotation, or how to get a haploid genome sequence into a diploid genome mapping framework.

Stefan Prost, PhD
Department of Integrative Biology
University of California Berkeley
Berkeley, CA 94720-3140
USA
Email: stefanprost.research@protonmail.com
Email: stefan.prost@berkeley.edu
Twitter: @stefanprost

Stefan Prost is a postdoc at the Senckenberg Museum in Frankfurt, Germany, working on conservation and evolutionary genomics. His research focuses on applied conservation genomics, investigating the basis of evolutionary processes such as adaptation and speciation, and portable sequencing technologies. Over the years he has worked with each commercially available sequencing technology and researched combinations of sequencing technologies, sequencing library types and bioinformatic processing to generate high quality reference genomes.

Assembly Workshop

November 10-11 2018, University of Montana Campus

Interdisciplinary Sciences Building (ISB) 110

Registration Information

Internal UM Students and Staff, Affiliate, and ConGen 2018 Attendees

$200.00, with a discounted fee for each additional registrant for each individual lab

External

$300.00

Please fill out the registration form here

•  External registrants will need to Pay by check or credit card,
  • Please upload the Payment form.
• Please direct any inquiries to Tamara Max (tamara.max@umontana.edu)

• The DoubleTree Inn is a popular location for our visitors. Located right on the Clark Fork River across from UM. The walk is just less than 1 mile to the workshop.

• The Holiday Inn is a popular location for our visitors. Located right on the Clark Fork River. It is a beautiful walk along the Clark Fork River (approximately 1 mile), or they may provide shuttle service to the workshop.

• Goldsmith's Inn B&B is a nice place to stay. 

• The Campus Inn was another suggestion from some of our attendees.

Missoula International Airport is the closest airport to the city of Missoula

Taxi/Shuttle service

Taxi:

Missoula Green Taxi (406) 728-8294

Yellow Cab of Missoula (406) 543-6644

Missoula is also serviced by both Uber and Lyft

Hotel Shuttle service (for selected hotels)

Double Tree Inn (406) 728-3100

Holiday Inn Express (406) 830-3100

Public Transit

Mountain Line Transit: Zero Fair Bus System