This in-person workshop is jointly hosted by LIC, Genomics Aotearoa and NeSI. It is for New Zealand scientists and will explore genotype imputation techniques.  Genotype imputation is a cost-efficient approach to approximate high-density genotypes or full sequence data from low-density genotypes/low-pass sequencing data of individuals. This workshop is intended for anyone interested in learning how to use either Beagle or Minimac to impute genotypes and how to evaluate the imputation performance of these methods.

This workshop will involve:

• A brief overview of imputation.
• Quality control and preparation of genetic data for imputation.
• Evaluation the imputation performance using different parameters.
• Workshop attendees will observe demonstrations and then work through exercises.

Prerequisites: Attendees are expected to have some familiarity with basic bash and R. If you would like a refresher, you can find a copy of past workshops which cover the fundamentals of bash (here) and R (here). Additionally, to get the most out of this workshop attendees are encouraged to know about basic genetics and genomics.

Setup: This is a hands-on workshop. The 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 machine to work on and plan to participate actively in the workshop. You will require a working web browser.

Sign up to the workshop at Eventbrite.

Genetics Otago together with Allan Wilson @ Otago is pleased to bring you the third Ira Rangahau Māori Symposium in July 2023. The inaugural Ira Rangahau took place in 2018, spearheaded by Associate Professor Phillip Wilcox (Ngāti Rakaipaaka, Rongomaiwahine, Ngāti Kahungunu ki te Wairoa). Since then, it has become a significant fixture in the Genetics Otago calendar. Building upon its success, the Ira Rangahau 2021 symposium saw the inclusion of Dr. Alana Alexander (Ngāpuhi: Te Hikutu, Pākehā) and Dr. Catherine Collins (Kāi Tahu, Pākehā) on the organising committee. This event expanded its reach by adopting a hybrid format, accommodating both in-person and online participation.

The 3rd Ira Rangahau Symposium will be held over a full day on the 10th of July 2023 on the Dunedin campus. This event will once again convene Māori kairangahau (researchers) from around the motu to present their genetics-related research spanning diverse domains from the primary sector to health, to whakapapa and te taiao (the environment). We also welcome another researcher to our organising committee, Dr Nathan Kenny (Te Ātiawa, Ngāi Tahu).

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 2nd of August, 2023, and is for New Zealand researchers interested in learning to write scripts and submit jobs to an HPC using a scheduler. This workshop is an excellent follow-up for everyone who has recently completed the Introduction to R and Introduction to Bash workshops, although these are not strictly prerequisites. You are expected to have some knowledge of basic terminal commands.

The following topics will be covered:

– Designing a variant calling workflow.
– Automating a workflow.
– An introduction to HPC.
– Working with job scheduler.

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.

Training workshop: Intermediate Shell for Bioinformatics
Tuesday, July 18, 10am – 4pm, online
This workshop is hosted by Genomics Aotearoa and NeSI and is for New Zealand researchers interested in progressing their abilities with Shell.

The workshop will include:

An overview of the Shell, UNIX and Linux.
Downloading data from a remote source and checking data integrity.
Recap navigating files and directories, and commands used in routine tasks.
Inspecting and manipulating data, part 1 (the head, less, grep, and sed commands).
Inspecting and manipulating data, part 2 (using awk and bioawk to process text).
Automating file processing.
Challenges: solve example molecular biology problems using shell scripts.
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 of 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.
And have a basic understanding of:

File/directory permission in Linux.
For loops (preferred, not required).
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. The 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 one week prior to the workshop.

You can view the workshop material, including the objectives and content, here: https://genomicsaotearoa.github.io/shell-for-bioinformatics/

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

Register for this workshop at Eventbrite

If you have any questions about this workshop, including whether it is suitable for you, please contact tyler.mcinnes@otago.ac.nz.

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.