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Genome Assembly Workshop Part II: Bioinformatics (9/26/2017)

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Koshland Hall

238

Berkeley, CA 94720

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Workshop Outline:

Sept. 26, 2016

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 a 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.

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.

Date and Time

Location

Koshland Hall

238

Berkeley, CA 94720

View Map

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