This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 26th of July, 2023, and is for New Zealand researchers interested in learning to create and work with pangenome graphs.

This workshop will include:
– An introduction to pangenome graphs.
– Setup guide for using the tools and data in the workshop.
– Overview of the PGGB toolkit.
– Choosing parameters to construct a graph.
– QC
– Extracting variant data.
– Mapping short reads against a pangenome graph.

This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:
– Navigating files and directories.
– An understanding on full versus relative paths.
– Working with files and directories (examining files, creating, copying, moving and removing).
– Use a command line-based text editor such as nano.

If you lack the above skills, you can use these sites as a refresher:
– Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/

Setup
This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.
The material for this workshop can be previewed here.

Participants must have their own laptops and plan to participate actively. You will require a working web browser.
If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.

Register for this workshop at Eventbrite here.

Dovetail Genomics is organising a webinar with the title of “What is 3D genomics and why it matters”on 2^nd Aug. In this webinar, we explore the vital role of chromosome folding and spatial organisation in gene regulation, and its seamless integration with multi-omic strategies such as transcriptomics and epigenomics. Discover real-world applications of 3D Genomics in gene regulation and oncology, including oncogenic regulation in multiple myeloma and enhancer hijacking in prostate cancer. Plus, learn how to effectively incorporate 3D Genomics into your research.

What you’ll learn:

• How 3D Genomics fits into the multi-omic toolbox (including ChIP-seq & ATAC-seq).
• What information 3D Genomics uniquely unlocks.
• Why integrating 3D Genomics provides valuable insight into your research.

Speaker: Cory Padilla, Ph. D., Product Manager, Dovetail Genomics, part of Cantata Bio

DTG Webinar_2nd Aug

Department of Zoology Friday Seminar:  4th August, 12:00pm, Zoom

Invasive species, and the secrets they can teach us about the genetics of local adaptation.

Katarina Stuart (School of Biological Sciences, University of Auckland)

Invasive species present an invaluable opportunity to explore how organisms may cope with dramatic environmental shifts. Invasive species are introduced to new ranges, and must quickly respond to the new selection pressures in a process termed ‘rapid adaptation.’ At the same time, invasive species often undergo a genetic bottlenecking during translocation, which may cause a reduction of diversity in the population due to a loss of rare genetic variants. By studying the genetic shifts invasive populations have undergone, we may begin to understand better how genetic diversity supports a population’s ability to survive. In particular, ongoing developments in sequencing and analytical tools are enabling more comprehensive characterization of diverse components of genetic diversity present in natural populations. Here, we examine the invasion story of a well known avian pest, the common myna (Acridotheres tristis). Using whole genome resequencing we explore the impacts of successive bottlenecks on genomics variation, comparing patterns across a diverse range of different genetic variants, which include single nucleotide polymorphisms, structural variants, and transposable elements. With such data, we hope to better understand how components of genetic variation contribute to adaptive potential in an invasive population, as this has important implications not just in invasive species management and forecasting, but also in conservation efforts focused on vulnerable and managed native species.

Friday 4^th August, 12:00pm

In-person hub: Benham seminar room (B215)

Zoom link: https://otago.zoom.us/j/97890882533?pwd=R0l0SXowNy9nTE02T21RZWUybjVoQT09

Meeting ID: 978 9088 2533

Password: 798823

Species-wide genomics of kākāpō provides transformational tools to accelerate recovery

A reminder about our Genomics Aotearoa seminar, online this Friday, August 4 at 3pm.

We welcome Dr Joseph Guhlin (University of Otago) to talk about Species-wide genomics of kākāpō provides transformational tools to accelerate recovery.

Please invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there. Questions and discussions are welcome.

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

About Joseph
Dr Joseph Guhlin graduated with a PhD in Plant & Microbial Sciences from the University of Minnesota.

Based at the University of Otago, he is working in the Genomics Aotearoa High Quality Genomes and Population Genomics programme. A programmer by trade, he is interested in small pop genomics, high-performance computing, gene family expansion and contractions, and applying machine learning to small populations and genetics.

This in-person workshop is delivered by Genomics Aotearoa and NeSI, and will be taught over two consecutive days on 9-10 August 2023 from 10am-4pm NZT. It is for New Zealand researchers interested in signals of selection in genomes.

Sign up to this workshop at Eventbrite.

The focus of this workshop is on identifying signals of selection in an example genome using the outlier analysis method. Outlier analysis assumes that the majority of the genome is under neutral selection and some loci will appear as outliers relative to this background.

This lesson assumes learner has no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of selection. You are expected to have some familiarity with both the R programming language and with basic command line (bash). If you need to refresh, please revise the material in our previous workshops on R and bash.

We encourage you to bring your own data! For participants who do not have their own data, a group dataset is available and will be used by the instructors during the examples.

During this workshop you will:
Download example genomic data (or prepare your own).
Use the PCAdapt tool to identify outlier loci within a genome.
Use VCFtools to identify outlier SNPS in population comparisons.
Use Bayescan to identify outlier SNPS based on allele frequencies.
Relate identified SNPS to phenotypic variation.
Compare the results of the different methods and discuss the results.
Setup
This is an in-person, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

Participants must have their own laptops and plan to participate actively. You will require a working web browser.

If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.

Tyler McInnes
Training Coordinator, Genomics Aotearoa
www.genomics-aotearoa.org.nz

Webinar: 3D Genomics Experimental Considerations

Aug 10, 2023 3:00 PM (Auckland)

Join us for an insightful talk on 3D Genomics, where we will walk you through what is involved in designing and running a 3D Genomics experiment in the lab, sharing tips and best practices. We will also highlight how to QC the library, and what resources are available to navigate data processing. There will also be an opportunity to ask questions to our expert scientist.

What you’ll learn:

• How to design a 3D Genomics experiment.
• What is involved in running a 3D Genomics experiment in the lab.
• How to navigate data processing and QC analysis.

Speaker: Myriam El Khawand, Ph.D. 

Senior Customer Success Scientist

Dovetail Genomics, part of Cantata Bio

DTG Webinar_10 Aug

There are 20 fully funded positions available on the program.

The program is open to Māori (tauira, kaitiaki, kaipakihi) who want to better understand the opportunities and challenges associated with māori data science, māori data sovereignty, as well as key technical, cultural and ethical issues.

Applications will be considered from university students in any discipline as well as people with strong iwi, community or business background.

Applications will close Sunday 16 July 2023.
https://www.indigidataaotearoa.com/

Unravelling Gene Regulation with the Dovetail Pan Promoter Panel

Advancements in genomics have revolutionized our understanding of gene regulation, paving the way for ground-breaking discoveries in various fields, from developmental biology to disease research. At the forefront of this transformative landscape is the Dovetail Pan Promoter Panel, a genomics tool designed to unravel the intricacies of gene regulation.
In this seminar, we invite you to embark on a journey into the world of regulatory genomics and explore the power of the Dovetail Pan Promoter Panel. Led by renowned experts in the field, this seminar will delve into the unparalleled capabilities of the panel and its potential to unlock the hidden secrets of gene expression.

Date: 30th August, 2023
Time:3:00 PM – 5:00 PM (Auckland, NZ)

Speaker 1: Professor Yasuhiro Murakawa
Kyoto University Institute for Advanced Study (KUIAS)
Dissecting human disease pathways using high-resolution chromatin contact maps
Large-scale genome-wide association studies (GWAS) have yielded an increasing number of disease-associated genomic loci. However, the functional interpretation still largely remains unclear. Recently, it has become apparent that disease-associated genetic variants are often found within enhancers. Enhances act to strongly enhance the expression of their target genes in a cell-type specific fashion, by physically associating with their promoters. We have developed a 5’-end single-cell RNA sequencing approach to comprehensively map active enhancers from heterogeneous helper T cells. By integrating with GWAS datasets, we identified hundreds of human enhancers associated with autoimmune diseases. To gain important clues to human disease pathways, here we used Micro-C as well as promoter-capture Micro-C, methods that can analyze chromatin interactions with super-high resolution. We systematically identified target genes of these enhancers, revealing novel human disease molecular mechanisms. In sum, we provide a general framework to investigate molecular mechanisms underlying human diseases.

Speaker 2: Myriam Elkhawand, Customer Success Manager, Dovetail Genomics
Setting up the Dovetail® Pan Promoter Assay in the lab
In this second talk, Myriam will delve into the details of Dovetail Pan Promoter protocol and library quality control measures that play a pivotal role in assessing the success of the assay. She will discuss best practices in carry out the assay, library QC, emphasizing the importance of stringent quality standards for reliable data analysis. She will also share the analysis pipeline for Dovetail Pan Promoter panels.

Pan Promoter Webinar_30 Aug

Nanopore Day, Queenstown 2023

Date: Thursday 31st August 2023
Venue: Queenstown, New Zealand
Time: 9:00 – 17:00

Hear about the latest technical updates for Oxford Nanopore Technologies as well as talks from local scientists about their latest work using nanopore technology.

There will also be an opportunity to submit questions throughout the talks, which will be answered in the Q&A sessions following each presentation.

Please note that this is an in-person event.

There is no delegate fee for this event, but registration is required at https://nanoporetech.com/event/NanoporeDayQueenstown

Your place at this event will be confirmed via email from events@nanoporetech.com.