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1. Exploring the mouse genome in Ensembl and Previewing GRCm39: assembly updates from the GRC (Andrew Berry, Emily Perry, and Tayebeh Rezaie)

The Ensembl-HAVANA team produce manual gene annotation for the human and mouse genomes as part of the Gencode project. We will present the Gencode geneset and explain how this is produced. This workshop will provide a brief introduction to the Gencode geneset in the Ensembl genome browser (www.ensembl.org) followed by hands-on demonstrations and exercises that describe and demonstrate an adaptable workflow for exploring and exporting genomic data with a focus on mouse. Workshop materials, including slides, demonstration screenshots, exercises, and solutions will be made available before the workshop and will remain permanently online at our training portal: https://training.ensembl.org.

The Genome Reference Consortium (GRC), the group responsible for continued development of the mouse reference assembly will discuss the latest improvements to the mouse reference genome assembly, focusing on (1) summary of assembly updates since the 2012 release of GRCm38, (2) analyses of the next coordinate-changing update (GRCm39) planned for release in late 2019/early 2020 which demonstrate remarkable increased assembly contiguity and precision, (3) ongoing work to improve RefSeq annotations, and (4) GRC website (www.genomereference.org/) resources and mechanisms for contacting the GRC with assembly questions and curation requests and (5) our future curation activity post release of GRCm39.

For more information please see https://docs.google.com/document/d/1Id4Z4RQlzKNXHZgm9wxbhTubN-SNUby48zCnsxgXF0g/edit?usp=sharing

2. Next Generation Sequencing presented by Thomas Keane

Next generation sequencing has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to assess and analyse the large volumes of sequencing data produced by next generation sequencers. This introduction to next generation sequencing bioinformatics course aims to equip participants with the essential skills and knowledge required to begin analysing next generation sequencing data and carry out some of the most common types of analysis. This tutorial will cover the algorithmic theory and principles of bioinformatics (data QC, alignment, and variant calling), with a strong focus on practical knowledge to use sequence analysis techniques and tools applicable to any species or genome size.
Modified version from the full course webpage at https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=719

3. Using International Mouse Phenotyping Consortium (IMPC) data , presented by Ann-Marie Mallon

The IMPC is generating multi-dimensional phenotyping data for each protein-coding gene. With data for over 6,000 mouse knockout lines now available, this resource is valuable for a wide range of researchers, not just those working in mouse. This workshop will provide an introduction to the IMPC, including an overview of the various phenotyping tests (https://www.mousephenotype.org/impress/), followed by an interactive session detailing how to use and understand the freely-available data in the IMPC portal, www.mousephenotype.org. Attendees with come away with a clearer understanding of what the IMPC is, how best to search for information on their genes or phenotypes of interest, and what the data actually means.

4. GeneWeaver  presented by Jason Bubier and Joel Richardson

GeneWeaver presentation and tutorial demonstration, presented by Jason Bubier

Systems genetics has been an effective strategy for gene discovery and for finding the relations among traits and their mechanisms in genetic reference populations. Integrative functional genomics combines data from diverse experimental paradigms to find the common and distinct biological mechanisms of biological traits within and across species. As these methods have evolved, so too have the software systems that support interactive user initiated analyses. Flexible tools have made rapid interrogation of integrative genetic and genomic data resources possible.
Participants in this workshop will have an opportunity to use the latest version of GeneWeaver for integrative genetic and genomic analyses. GeneWeaver allows users to integrate heterogeneous functional genomics data in an interactive manner. Participants will be guided through simple tutorial demonstrations to use GeneWeaver. Following the introductory tutorial demonstrations, participants will have an opportunity to pose questions related to their own specific research questions or work on challenge problems provided by the organizers.

Exploring multiple mouse genome with MGI’s Multiple Genome Viewer, presented by Joel Richardson

The availability of annotations for the sequenced genomes of 19 mouse genomes represents an unprecedented opportunity to investigate the relationship between genotype and phenotype in the laboratory mouse. To provide the research community with new tools to explore multiple genomes at one time, MGI and MouseMine implemented new user interfaces to take advantage of these data, including the Multiple Genome Viewer (MGV). MGV supports browsing and comparing multiple genomes simultaneously. With it, users are able to explore the annotated mouse genomes in a coordinated, parallel fashion not possible in other browsers. Key features include a highly interactive display (organized as a stack of horizontal strips, one per selected genome, with vertical connectors between the same/equivalent gene in each genome); the ability to find “equivalent” regions across selected strains; synchronized zooming and scrolling; the ability to find genes by disease, phenotype, or other association; and the ability to define and highlight lists of genes.  We recently released a preview of version 2 of MGV which offers significantly greater functionality, including the display of gene model structures, ability to zoom to the sequence level, the ability to download selected sequences from across genomes, the ability to download images, and numerous settings to control the display. Workshop participants will be introduced to MGV, its basic concepts and user interactions, and will work through several guided use-cases. There will be ample time for free exploration, questions, and discussion. As well, we are particularly interested in soliciting user feedback on this pre-release version.

5. Workshop: Easi-CRISPR: CRISPRing Made Easier presented by C.B. Gurumurthy, University of Nebraska Medical Center, USA