Links for AGBT talk

13 Feb 2016

References for AGBT 2016 talk

1. Joseph Bore operating a MinION in Nongo, Guinea.

• Bill Gates’ tweet
• The Verge article

2. Make research open access

• Yozwiak, Schaffner, Sabeti. Nature: Data sharing: Make outbreak research open access

3. Size of the MinION

• Loman, Quinlan Poretools: a toolkit for analyzing nanopore sequence data.
• Quick, Quinlan, Loman. A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
• Urban, J et al. Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION
• Risse J et al. A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

4. Behind the scenes

• http://lab.loman.net/2016/02/03/behind-the-paper-real-time-portable-sequencing-for-ebola-surveillance/

5. Packing up

• http://www.nature.com/nature/journal/v530/n7589/fig_tab/nature16996_SF2.html

6. Lab-in-a-suitcase

• http://www.nature.com/nature/journal/v530/n7589/fig_tab/nature16996_F1.html

7. Sierra Leone project

• http://virological.org/t/direct-deep-sequencing-in-sierra-leone-yields-73-new-ebov-genomes-from-february-may-2015/134

8. Portable Internet

• Brck Rugged Internet Hotspot
• Project Loon

9. Duration of sequencing runs

• Duration of sequencing runs

10. Validation

• Clustering of Illumina strains
• Blog post by Jared Simpson: Signal-level analysis of Illumina SNPs
• Original Nature Methods signal-level analysis algorithm

11. Real-time sequencing / Outbreak in context

• http://www.nature.com/nature/journal/v530/n7589/fig_tab/nature16996_F2.html

12. Ebola.nextstrain.org by Trevor Bedford and Richard Neher

• http://ebola.nextstrain.org

13. Sierra Leone analysis

• http://virological.org/t/update-on-ebola-virus-circulating-in-sierra-leone-and-guinea/151
• http://virological.org/t/recent-evolution-patterns-of-ebola-virus-obtained-by-direct-sequencing-in-sierra-leone/150
• http://virological.org/t/direct-deep-sequencing-in-sierra-leone-yields-73-new-ebov-genomes-from-february-may-2015/134

14. Tracking chains of transmission

• http://apps.who.int/ebola/current-situation/ebola-situation-report-21-october-2015

15. Frozen in time evolution

• http://www.virological.org private discussion forum
• http://www.nejm.org/doi/full/10.1056/NEJMoa1509773?rss=searchAndBrowse

15. Real-time digital pathogen surveillance

• Real-time digital pathogen surveillance: the time is now

16. Portable systems

• http://www.bento.bio
• Loose et al. Real time selective sequencing using nanopore technology.
• Palm PCR
• Cambio miniPCR

17. Transposome / offline base calling

• Simpson J, David M nanocall, in preparation
• Data will be uploaded when I get a better Internet connection.

Thanks for listening ;)