Travel Tips

Program

 

Day 1 December 6

(BMC lecture halls B8 and B10)

 

8:30 – 8:55      Registration. B10.

Symposium in B8:

9:00 – 9:05    Welcome note. Jessica Nordlund, NGI.

9:05 – 9:25      What is the latest in Long-Read Sequencing technologies at NGI? Olga Vinnere Pettersson, NGI.

 

SESSION 1 – INTRODUCTION to technologies and research highlights. B8. CHAIR: Jessica Nordlund.

9:25 – 9:50       Company presentation: PacBio. Gerrit Kuhn: Latest Capabilities & Future Directions of PacBio’s Long-Read SMRT Sequencing Technology.

9:50 – 10:15      Company presentation: 10X Genomics. Annika Branting: Linked-Reads and Single Cell Gene Expression for Improved Genomics.

10:15 - 10:40     Company presentation: Oxford Nanopore. Richard Compton. Title TBA. Taking long-read sequencing into production scale with Oxford Nanopore.

 

10:40 – 11:00    Coffee break, B10

 

SESSION 1, continued: INTRODUCTION to technologies and research highlights. B8. CHAIR: Jessica Nordlund.

11:00 – 11:30     KEYNOTE SPEAKER - Jason Underwood, Uni Washington. What Made Us Human?  A High Resolution Look at Humans & the Great Apes.

11:30 – 11:50      Adam Ameur, NGI. Filling gaps in the human reference with sequences from two Swedish individuals.

11:50 – 12:10      Carl-Johan Rubin, Uppsala University. Exploring vertebrate genomes using several long-read sequencing methods.

12:10 – 13:15       Lunch at B10. Company booths open for presentations.

 

SESSION 2: Human genomics & medicine, B8  CHAIR: Adam Ameur.

13:15 – 13:45      KEYNOTE SPEAKER - Robert Sebra, ICANH School of Medicine, Mount Sinai Hospital. Emerging Long Read Technologies Toward Highly Resolved Translational Research.

13:45 – 14:05     Anna Lindstrand, Karolinska Institute. Human structural variations for health and disease.

14:05 – 14:25     Sanna Gudmundsson, UU. Clinical applications of long read sequencing for phasing in inherited disorders.

14:25 – 14:45     Per Stenberg, Swedish Defense Research Institute. Assembly and bacterial identification using long-read sequencing.

 

14:45 – 15:15    Coffee, Company booths open for presentations. B10.

 

SESSION 3: Non-model organisms & biodiversity, B8 CHAIR: Adam Ameur

15:15 – 15:45     KEYNOTE SPEAKER -Graham Etherington, Earlham Institute. Reassembling roadkill– the long and the short of the European Polecat.

15:45 - 16:05    Matt Webster, Uppsala University. A chromosome-level hybrid assembly of the honeybee genome.

16:05 – 16:25    Maria Strandh, Lund University. A whole-genome approach to resolving the complex MHC region in a songbird - the Great reed warbler.

16:25 – 16:45    Magnus Alm Rosenblad, Gothenburg University. Experiences from marine non-model organism genome projects.

 

16:45 – 16:50     Short break

 

16:45 – 17:30  Panel Discussion with representatives of PacBio, 10x, Oxford Nanopore and NGI. B8. MODERATOR: Jessica Nordlund.

 

17:30 - 18:30 Mingle and bar. B10.

 

 

Program for Day 2. December 7

(Trippelrummet at Navet)

 

9:00 – 9:05    Introduction to Day2 workshops. CHAIR: Adam Ameur.

9:05 – 9:30     SESSION 1: DNA extractions, sample quality requirements and pre-sequencing sample manipulation

Olga Vinnere Pettersson and Mai-Britt Mosbech, NGI-Uppsala. My sequencing result is not what I expected. What went wrong?

9:30 – 10:00    SESSION 2: De novo assembly with long reads

9:30 – 9:45    Henrik Lantz, NBIS. De novo assembly: a point of view from the National Bioinformatics Infrastructure - Sweden.

9:45 – 10:00  Remi-André Olsen, NGI-Stockholm. The challenges and opportunities of de novo sequencing using 10X linked-reads.

10:00 – 10:30 Coffee and informal discussions

 

10:30 – 10:50   SESSION 2: Combining data from different technologies

10:30 – 10:40 Mats Pettersson, Uppsala University. Combination of Hi-C and long-read data for de novo assembly of Atlantic herring.

10:40 – 10:50 Oskar Karlsson Lindsjö, SLU. From pooping pigs to PacBio – Improved bacterial genomes in clinical microbiology.

10:50 – 11:35 SESSION 3: Targeted sequencing & Structural variation

10:50 – 11:05 Vanja Börjesson, KI. Pipeline for detection of structural variants using 10X-genomics data.

11:05 – 11:20  Adam Ameur, NGI-Uppsala. Targeted enrichment for Long-Read technologies. Title TBA.

11:20 – 11:35  Marie Just Mikkelsen, Samplix. PINS: a novel method of target enrichment for long-read sequencing.

11:35 – 12:00 Discussion

12:00 - 13:00  Lunch and informal mingle

 

13:00 – 16:00  SESSION 5: Bioinformatics. Company-provided workshops on respective technology

13:00 – 14:00  PacBio. Philip Lobb. Adventures in SMRT Sequencing: Leveraging Single Molecule Accuracy.

14:00 – 14:10   Short break

14:10  – 15:10   10x Genomics. Alvaro Martinez Barrio. Computational Pipelines for Linked-Reads at 10x Genomics.

15:10 - 15:30  Coffee and informal discussions

15:30 – 16:30  Oxford Nanopore. James Platt. Real-time long-read sequencing right here, right now.

 

16:00 - 16:30    Closing the event. Short break.

16:30 - 18:00    On demand: further discussions with company representatives and NGI personnel.