Bioinformatics Spring School 2024

About

Hosted at the University of Otago, the Bioinformatics Spring School 2024 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:

Matt Bixley (NeSI)
Professor Mik Black (Biochemistry)
Dr Murray Cadzow (Research and Teaching IT Support)
Dr Ludovic Dutoit (Zoology)
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, 18-22 November 2024
University of Otago, Dunedin, New Zealand

This is an in-person event.

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
RNAseq Analysis
eDNA Analysis

along with computational topics such as:

Introduction to the Unix commandline (Bash)
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 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

Expressions of interest applications are now open and will close midnight, Friday 29th September 2024.

Please register your interest in attending by filling out this form

Applications close midnight Sunday 29th September 2024 anywhere on earth. 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

RNA Seq

Explain what RNA-seq is.
Describe some of the most common design choices that have to be made before running an RNA-seq experiment.
Provide an overview of the procedure to go from the raw data to the read count matrix that will be used for downstream analysis.
Show some common types of results and visualizations generated in RNA-seq analyses.

eDNA

Bioinformatically analyse metabarcoding data using a cutadapt/vsearch pipeline
Build a custom reference database using CRABS
Assign taxonomy using 3 different classifiers, including BLAST, SINTAX, and IDTAXA
Conduct data curation using tombRaider to remove PCR artefacts and pseudogenes
Basic statistical analyses and visualisations in R

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 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 18th Nov

Time	What
09:30	Welcome
10:00	Introduction to NeSI
10:45	Break
11:05	Introduction to BASH
12:15	Lunch
13:00	Keynote: Associate Professor Phillip Wilcox - Māori Genomic Data
14:15	Break
14:35	Intro to R
16:30	End of Day

Tuesday 19th Nov

8am Breakfast (own cost) for those who signed up

Time	What
09:30	Speaker:
10:00	DNA variant calling
10:40	Break
11:00	DNA variant calling cont.
12:15	Lunch
13:00	DNA variant calling cont.
14:30	Break
14:50	DNA variant calling cont
16:30	End of Day

Wednesday 20th Nov

Time	What
9:30	Speaker
10:00	Long Read Assembly
11:00	Break
11:15	Long Read Assembly cont.
12:15	Lunch
13:00	Long Read Assembly cont.
14:45	Break
15:00	Long Read Assembly cont.
16:30	End of Day

Genome Assembly Lesson: https://otagobioinformaticsspringschool.github.io/long-read-assembly/

Thursday 21st Nov

Time	What
9:30	Speaker
10:00	eDNA
11:00	Break
11:20	eDNA cont.
12:15	Lunch
13:00	eDNA cont.
14:40	Break
15:00	eDNA cont.
16:30	End of Day

eDNA lesson: https://otagobioinformaticsspringschool.github.io/2024-edna/

Friday 22nd Nov

Time	What
9:30	Speaker
10:30	RNAseq
11:00	Break
11:20	RNAseq cont.
12:15	Lunch
13:00	RNAseq cont.
14:40	Break
15:00	RNAseq cont.
16:30	End of Day

RNAseq lesson: https://otagobioinformaticsspringschool.github.io/bioc-rnaseq/