Bioinformatics Spring School 2022

COVID-19 Considerations

This is an in-person event and will take the appropriate COVID-19 mitigations as determined based on requirements/advice at the time of the event.

This may include (but not limited to):

Negative rapid antigen test before attending
Wearing of masks
Use of hand-sanitiser regularly
Maintaining social distancing

If you are sick it is expected you stay home.

About

Hosted at the University of Otago, the Bioinformatics Spring School 2022 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 of DNA variant calling, Genome assembly, environmental DNA (eDNA), and Nanopore.

This event is organised by:

Dr Alana Alexander (Anatomy)
Matt Bixley (NeSI)
Professor Mik Black (Biochemistry)
Dr Murray Cadzow (Research and Teaching IT Support)
Dr Ludovic Dutoit (Zoology)
Dr Natalie Forsdick (Manaaki Whenua - Landcare Research)
Dr Gert-Jan Jeunen (Anatomy)
Dr Tyler McInnes (Genomics Aotearoa)
Dinindu Senanayake (NeSI)

Please email murray.cadzow@otago.ac.nz for futher information/queries.

When and where?

9:30 - 16:30, 21 November - 25 November 2022
University of Otago, Dunedin, New Zealand

This is an in-person event. There will be COVID-19 mitigation measures in place determined by the requirements/advice at the time of the event.

Day	Topic
Monday	Introduction NeSI / Bash / R
Tuesday	Genomic variant calling
Wednesday	Genome assembly
Thursday	Environmental DNA
Friday	Nanopore

Cost?

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.

Is this for me?

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:

DNA variant calling from next generation sequence data
Genome assembly
Environmental DNA analysis

along with computational topics such as:

Introduction to the Unix commandline (Bash)
Introduction to R
Introduction to working in a high performance computing environment (provided by NeSI)

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 interleave 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.

Registration of Interest

Applications closed midnight 31st August (NZ). Applicants will be notified of their outcome the week following the close of applications.

Curriculum

Bioinformatic topics

DNA variant calling from next generation sequence data

Project organisation
Assessing read quality
Trimming and filtering
Variant calling workflow
Automating a variant calling workflow

Genome assembly

Genome assembly with long and short reads
Draft assembly
Assembly QC

Environmental DNA analysis

Next-generation sequencing approaches for environmental samples (metabarcoding)
Demultiplexing and quality assessment of NGS amplicon data
Clustering and denoising of sequence data
Determine species composition of samples (taxonomic assignment)
community ecology statistics for eDNA results

Nanopore

Base calling
Quality control
Variant calling

Computational Topics

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.

Introduction to the Unix command line (Bash)

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:

Navigating around the filesystem (files/directories/folders)
Running command line based programs
Creating scripts to automate workflows

Introduction to R

Analysis portions of the workshops will be performed using R. As such we will provide a brief introduction to R. This will include:

How to interact with R
Creating objects
How to use functions
How to install and use packages

Introduction to working in a high performance computing environment

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:

What/who is NeSI
Logging onto a remote computer
Transfer of data to/from a remote computer
What is a job scheduler and how to use it
How to request a project allocation on NeSI

Draft daily schedule

Monday 21st Nov

Time	What
09:30	Welcome
10:00	Introduction to NeSI
10:45	Break
11:00	Keynote
12:15	Lunch
13:00	Introduction to BASH
14:45	Break
15:00	Introduction to R
16:30	End of Day

Tuesday 22nd Nov

Time	What
09:30	Speaker
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

Wednesday 23rd Nov

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
TBA	Social activity
TBA	Dinner

There will be an optional social activity followed by a dinner for those who wish to join in. Dinner is pay your own way.

Thursday 24th Nov

Time	What
09:30	Symposium
10:30	Break
10:45	Experimental Design
11:00	QC and Denoising/Clustering
12:15	Lunch
13:00	Taxonomy Assignment
14:30	Afternoon Tea
14:45	Statistical Analysis
16:15	Course Summary
16:30	End of Day

Friday 25th Nov

Time	What
09:30	Speaker
10:00	Nanopore
10:45	Break
11:00	Nanopore cont.
12:15	Lunch
13:00	Nanopore cont.
14:30	Break
14:45	Nanopore cont.
16:30	End of Day