Featuring real-time NanoPore MinION and data analysis
The assembly workshop was developed by Dr. Stefan Prost and has been taught numerous times at Universities such as Stanford, Ohio State, UC Berkeley and also at international conferences and the Smithsonian institute in Washington DC. In this workshop Dr. Prost will cover the basics of genome assembly up through downstream analyses. Topic coverage will include:
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Stefan Prost, PhD
Department of Integrative Biology
University of California Berkeley
Berkeley, CA 94720-3140
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.
Tentative schedule, please check back as we refine our workshop content
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.
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.
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.
In this section, I will talk about tools used to assess, as well as, improve sequencing read quality.
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).
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.
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.
In this section, I will briefly discuss the pros and cons of Physical and Optical Mapping methods (such as BioNano’s Iryis platform).
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.
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.
November 10-11 2018, University of Montana Campus
Interdisciplinary Sciences Building (ISB) 110
Internal UM Students and Staff
Please fill out the registration form here