COVID-19 Considerations

This event will only proceed if Dunedin is under Alert level 1 or 2 onwards from Sunday 21st November.

Should Dunedin be operating under the COVID-19 protection framework (traffic light system), COVID-19 vaccination certificates may be required.

Key points:

• If you are sick don’t come
• QR scanning or manual sign-ins are required
• Masks will be worn
• Use hand-sanitiser regularly
• Maintain social distancing (Uni guidelines say 2m for those outside your normal work building/bubble + mask)

Travel from outside Dunedin

From the current guidelines if you are travelling from outside of Dunedin:

As at 21st November:

• Current location is Alert level 1 or 2 = come along
• Current location is Alert level 3 or 4 = stay home as inter-regional travel isn’t allowed

About

Hosted at the University of Otago, the Bioinformatics Spring School 2021 is a week long training event for researchers, supported by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI).

We will combine talks from researchers and hands on computational workshops (influenced by The Carpentries), covering example workflows of DNA variant calling, genotyping by sequencing (GBS), RNAseq analysis, and environmental DNA (eDNA).

This event is organised by:

• Dr Alana Alexander (Anatomy)
• Assoc Prof Mik Black (Biochemistry)
• Dr Murray Cadzow (Research and Teaching IT Support)
• Dr Hugh Cross (Anatomy)
• Dr Ludovic Dutoit (Zoology)
• Dr Ngoni Faya (Genomics Aotearoa)

When and where?

• 9:30 - 16:30, 22 November - 26 November 2021
• University of Otago, Dunedin, New Zealand

This is an in-person event.

Day	Topic
Monday	Introduction NeSI / Bash / R
Tuesday	Genomic variant calling
Wednesday	Genotype-by-sequencing
Thursay	Environmental DNA
Friday	RNA sequence analysis

Cost?

This event will only cost your time (there isn’t a $ charge).

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
• Genotype-by-Sequencing analysis (i.e. RAD-Sequencing)
• RNA-sequencing differential expression analysis
• 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.

The underlying workshop content is extremely similar to previous workshops run by Genomics Aotearoa so if you’ve already attended the Genomic Data Carpentry and RNAseq workshops you will have already covered the majority of the content.

Registration

Expressions of interest are CLOSED.

Expressions of interest closed 5pm 1st September (NZ). All applicants were emailed by 15th September if they were successful or not. If you didn’t receive an email please get in touch.

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

Genotype-by-sequencing analysis (RAD-Sequencing)

• Data quality assessment
• Calling variant workflow using Stacks (with or without a reference genome)
• Basic population genetic analyses (population structure, phylogenetic tree)

RNA-sequencing differential expression analysis

• Quality assessment
• Trimming and filtering
• Mapping and count
• Differential expression
• Overrepresentation analysis

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

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 22nd Nov

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

Tuesday 23rd 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
TBA	Social activity
TBA	Dinner

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

Wednesday 24th Nov

Time	What
9:30	Speaker
10:30	Data101: From raw data to individual samples files
11:00	Break
11:15	Calling SNPs de-novo
12:15	Lunch
13:00	Calling SNPs de-novo, discussion
13:30	Calling SNPs with a reference genome
14:30	Break
15:00	Evolutionary Genetics basic toolbox (Population structure, Phylogenetic tree)
16:30	End of Day

Thursday 25th 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 26th Nov

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