Links for IMMEM talk
12 Mar 2016References for IMMEM 2016 talk
1. Joseph Bore operating a MinION in Nongo, Guinea.
2. Make 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
5. Packing up
6. Lab-in-a-suitcase
7. Sierra Leone project
8. Portable Internet
9. 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
12. Ebola.nextstrain.org by Trevor Bedford and Richard Neher
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
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
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 ;)