Attending

Wrap up

  • Our presentation recordings are available here on YouTube
  • This the link to the google shared folder. Please make sure to make a copy if you would like to keep everything. Have a browse. In case you are looking for something you cannot find please let us know.
  • This is the link to the presentations subfolders. I got most presentations there. The naming convention is as follows: YYYYMMDD_PRESENTER.xxx. Some are missing, so if you want to add yours as well please stick to the naming convention. 
  • Most protocols are up on protocols.io. I am sure John and Ash will make theirs available soon as well. Thanks! I would recommend to join the group and post your protocols. The community lives of community contributions.
  • Tim Kahlke made a great long-read bioinfo tutorial here. Thanks!
  • Group photo

 

Schedule

Our workshop is more geared towards best parctices in HMW DNA, while providing an overview into different aspect of long-read sequencing and HiC analysis as well. The workshop is also hands-on heavy. Yet not everyone will be able to do everything and so we will need you to fill in the following quick questionnaire so we can best match you up in groups and pairs.

Monday to Wednesday will be wet-lab focused. Thursday and Friday will be analysis-focused. Download full Program here.

DNA extraction will be performed in groups and within groups people will work in pairs. The analysis part is also best done paired up. Research has shown that people learn better in groups and pairs so we will follow this idea during this workshop. Who knows, you might form new collaborations and friendships! 

Throughout the workshop we will have a range of exciting talks open to everyone that will be live-streamed via Zoom. We will also have two social events - one on Wednesday afternoon and one Friday to round the week off.

Workshop talks 

Eucalyptus Seminar Room (open to everyone). Download Talks Program here.

Title

Presenter

Day

Time AEDT

Zoom

Local time

Old is new: maximizing read lengths and yield for genome assembly

John Tyson

11/11

9:30 AM

Zoom

Local time

DNA quality requirements for Single-Molecule sequencing

Olga Vinnere Pettersson

11/11

5:00 PM

Zoom

Local time

Modern kits for long-read DNA extraction

Circulomics

12/11

9:00 AM

Zoom

Local time

Towards automation of high molecular weight DNA extraction

Claremont Biosolutions

12/11

9:30 AM

Zoom

Local time

SMRT sequencing: Highly accurate and affordable long-read sequencing with PacBio Sequel II

PacBio

12/11

2:00 PM

Zoom

Local time

Introduction to Nanopore Sequencing

Nanopore

12/11

2:30 PM

Zoom

Local time

Optimizing Nanopore sequencing runs with challenging tissue types

Stella Losek

12/11

3:30 PM

Zoom

Local time

Long-read assembly using repeat graphs

Mikhail Kolmogorov

13/11

2:00 PM

Zoom

Local time

Mapping cDNA reads to transcriptomes and genomes

David Eccles

13/11

3:00 PM

Zoom

Local time

Single base-pair RNA modification and its involvement in human disease

Eva Maria Novoa Pardo

13/11

6:30 PM

Zoom

Local time

Overiew of HiC applications in human genetics and genome assembly

Sebastian Kurscheid

14/11

9:00 AM

Zoom

Local time

From Contigs to Chromosomes: Using proximity Ligation Data to Improve Genome and Metagenome Assembly

Phase Genomic HiC 

14/11

10:00 AM

Zoom

Local time

Introduction to data analysis

Tim Kahlke

14/11

11:30 AM

Zoom

Local time

Long read landscapes of 5-methylcytosine in liver pathophysiology

Chloe Goldsmith

14/11

5:00 PM

Zoom

Local time

Methplotlib: analysis of modified nucleotides from nanopore sequencing

Wouter De Coster

14/11

5:00 PM

Zoom

Local time

Short science talks

1:30 PM

Zoom

Local time

For reproducibility, we need the methods behind the data.

Lenny Teytelman

15/11

1:30 PM

 

 

Application of long read sequencing technologies to understand the evolution of fungal rust pathogensA

Figueroa, Melania

15/11

1:45 PM

 

 

The chromosome-scale assembly of the flax rust fungus: challenges of assembling a highly repetitive, dikaryotic genome

Jana Sperschneider 

15/11

2:00 PM

 

 

Complete genomes give new insight into old stories of horizontal gene transfer

Megan McDonald

15/11

2:15 PM

 

 

Genome assembly from a single Argentine stem weevil

Tom Hardop

15/11

2:30 PM

 

 

Long read Structure variants of plant genomes.

Scott Ferguson

15/11

2:45 PM

 

 

Strategies for assembling a massive spider genome

Sasha Mikheyev

15/11

3:15 PM

 

 

The Wolpertinger Genome – Genome Contaminations in publicly available Genome Assemblies

Tim Kahlke

15/11

3:30 PM

 

 

Phased methylomes resolve genomic imprinting in mice

Quentin Gouil

15/11

3:45 PM

 

 

Adventures in RNA and cDNA sequencing with Nanopore

Kirston Barton

15/11

4:00 PM

 

 

Things can only get better now…

Elena Hilario

15/11

4:15 PM

 

 

What to bring and do before the workshop

  • Please fill in this questionnaire by Thursday 7/11 12PM AEDT.
  • Please bring a laptop if available (we will have some spare but not for everyone).
  • If you bring your own laptop, please install Virtualbox (including the "Virtualbox Extension Pack) prior to the course.
  • Please bring an open mind and eagerness to learn.
  • Please don't bring excess work.
  • Please let benjamin.schwessinger@anu.edu.au know if you have applied long-reads and long-range analysis previously and want to give a quick science talk.

Expectations

Please keep in mind that the workshop is meant to provide a learning environment and is a community workshop. Everyone involved in this workshop does it for the 'love of it' and not for making money. We all donate time and energy to make this happen. So please be respectful to everyone during the workshop (instructors and follow participants). Things might not go perfect at times but this does happen in science, and might also happen during the workshop. Be kind.

The sequencing part of the workshop is not meant to provide you with extensive sequencing data for your genome project. You will have plenty of time to chat with world-leading experts about how to optimize your specific DNA extraction if needed. We promise the combined HMW DNA extraction 'IQ' during the workshop will not be beaten anywhere else in the world. So make best use of this. Watch, talk, engage, and learn. 

Venue

The workshop will be held in the RN Robertson Building, 46 Sullivans Creek Road, ANU. We will meet in the Eucalyptus Seminar Room on Monday morning. From the automatic glass front doors (the Little Pickle cafe will be on your right), go directly up the ramp to the second floor and head to the back of the building. We will provide morning and afternoon tea, and food and drinks for social events. Dietary requirements can be requested at registration. Lunch can be purchased at nearby Kambri (ANU Union).

Guest Wi-Fi

  • Network: ANU Secure
  • Username: EcoBioLaboratory
  • Password: EBL.LongRead

Parking

Information on parking at ANU can be found here. The closest carparks to the Robertson Building are Sullivans Creek carpark (Pay As You Go) and Union Court carpark (Ticket - coins and EFTPOS) - see ANU’s online visitor parking map.

Accomodation

For out-of-town participants we have secured a reduced room rate at the Canberra Rex Hotel ($135/night room & breakfast). The Rex is ~30 min walk from the ANU. If you would like to stay at the Rex please book by 18 October and let them know you are attending the 'Sequencing Workshop at ANU'.

Updated:  15 August 2020/Responsible Officer:  Director/Page Contact:  Coordinator