Hosted at the University of Otago, the Bioinformatics Spring School 2023 is a week long training event for researchers, supported by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI). This event is primarily targeted at researchers and students based in Aotearoa New Zealand. International applications will be considered but will need to be able to attend in-person.
We will combine talks from researchers and hands on computational workshops (influenced by The Carpentries), covering example workflows using short and long read DNA sequencing technologies for variant calling and genome assembly.
This event is organised by:
Please email murray.cadzow@otago.ac.nz for futher information/queries.
This is an in-person event.
| Day | Topic |
|---|---|
| Monday | Introduction NeSI / Bash |
| Tuesday | Genomic variant calling |
| Wednesday | Workflows and Reproducibility |
| Thursday | Genome Assembly |
| Friday | Nanopore |
This event itself will only cost your time (there isn’t a $ charge) and lunches will be provided. Attendees will need to fund all other travel related expenses.
This event is designed to give researchers (including students - 4th year and above) the opportunity to learn about and practice some bioinformatic skills. We’ll be covering bioinformatic workflows such as:
along with computational topics such as:
This week long event is designed to be an immersive experience so we ask that you commit to the entire week. We have chosen to interweave the computational topics throughout the week so that we can build on them throughout the entire week, so this ensures participants have the key knowledge at the right time.
Expressions of interest applications are now open and will close midnight, Friday 29th September 2023.
Applications closed midnight 29th September (NZ). Applicants will be notified of their outcome the week following the close of applications.
These topics will be integrated into the bioinformatics workshops and built upon across the week with the goal of demostrating a best practices workflow approach to Bioinformatics analysis.
Many bioinformatic programs will only operate in a Unix command line environment, as such we need to provide an introduction to working in this environment which will cover:
We’ll be making use of the New Zealand eScience Infrastructure (NeSI), which is the national provider of high performance computing for researchers, to run our analysis and as part of this we’ll cover:
Using automated version control systems such as git is an important aspect of computational research. We’ll cover:
Often for bioinformatic analyses we have a multistep series of computations. A useful tool to manage these workflows along with keeping track of inputs and outputs, are workflow managers such as snakemake. For this we’ll cover:
| Time | What |
|---|---|
| 09:30 | Welcome |
| 10:00 | Introduction to NeSI |
| 10:45 | Break |
| 11:00 | Keynote: Phil Wilcox |
| 12:15 | Lunch |
| 13:00 | Introduction to BASH |
| 14:45 | Break |
| 15:00 | BASH cont. |
| 16:30 | End of Day |
Evening: Penguins and sea lions outing for those who signed up
8am Breakfast (own cost) for those who signed up
| Time | What |
|---|---|
| 09:30 | Speaker: Anna Gosling |
| 10:00 | DNA variant calling |
| 10:45 | Break |
| 11:00 | DNA variant calling cont. |
| 12:15 | Lunch |
| 13:00 | DNA variant calling cont. |
| 14:30 | Break |
| 14:45 | DNA variant calling cont |
| 16:30 | End of Day |
Evening: Penguins and sea lions outing for those who signed up
| Time | What |
|---|---|
| 9:30 | Speaker |
| 10:30 | Introduction to Version Control |
| 11:00 | Break |
| 11:15 | Version Control cont. |
| 12:15 | Lunch |
| 13:00 | Reproducible pipelines |
| 14:45 | Break |
| 15:00 | Reproducible pipelines cont. |
| 16:30 | End of Day |
| Time | What |
|---|---|
| 9:30 | Speaker |
| 10:30 | Genome assembly |
| 11:00 | Break |
| 11:15 | Genome assembly |
| 12:15 | Lunch |
| 13:00 | Genome assembly |
| 14:45 | Break |
| 15:00 | Genome assembly |
| 16:30 | End of Day |
(Optional) Drinks/nibbles at own cost, 5pm Noisy Brewery - 7 Anzac Avenue, Central Dunedin, Dunedin.
| Time | What |
|---|---|
| 09:30 | Introduction to Nanopore Sequencing |
| 10:00 | Nanopore flowcell loading demo: Dr Augstine Chen |
| 10:15 | Basecalling with Dorado |
| 10:45 | BREAK |
| 11:00 | Basecalling continued |
| 11:30 | QC with Nanoplot and FastQC |
| 12:15 | LUNCH |
| 13:00 | Talk: Dr Michael Dunnet |
| 13:30 | Alignment and Variant Calling |
| 14:30 | BREAK |
| 14:45 | Adaptive sampling |
| 16:00 | FINISH! |