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London Calling: A Year of Happy MAPping 14th May 2015

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My talk on Oxford Nanopore MinION at London Calling meeting.

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London Calling: A Year of Happy MAPping 14th May 2015

  1. 1. A year of happy MAPping May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar Nick Loman
  2. 2. Breakfast meeting MinION is unique: • Real-time • Portable • Super long reads
  3. 3. A year of happy MAPping May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar Nick Loman
  4. 4. Lambda burn-in
  5. 5. Do you remember your first read? 10.6084/m9.figshare.1052996
  6. 6. One diagnostic read
  7. 7. poretools May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar
  8. 8. Outbreak May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar
  9. 9. Species ID Align MinION reads to taxa specific genes (MetaPhlA2) using LAST. S.enterica identified in under 30 mins Serogroup ID Align minION reads to S.enterica reference genome. Phylogenetic placement with pplacer Within 50 mins we could identify the strains as serotype Enteritidis
  10. 10. Outbreak ID Alignment of MinION reads to Salmonella Enteritidis reference genome. Phylogenetic placement with pplacer Within 100 minutes the outbreak strains was unambiguously part of the national 14b cluster (RED) and the sporadic cases (BLUE) was indeed sporadic Quick et al – Genome Biology in press
  11. 11. gigasciencejournal.com/content/3/1/22/
  12. 12. Nanocorrect biorxiv.org/content/early/2015/03/11/015552
  13. 13. E. coli single contig assembly biorxiv.org/content/early/2015/03/11/015552
  14. 14. Ebola May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar
  15. 15. http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3290.html
  16. 16. www.nature.com/nmeth/journal/v12/n4/full/nmeth.3327.html
  17. 17. http://www.nature.com/news/data-sharing-make-outbreak-research-open-access-1.16966
  18. 18. Dstl Protocol Development • Two approaches tried on archived Ebola RNA: – Genome tiling amplicon: RT-PCR – Direct metagenomics: Ebola-spiked sample • Validation with MiSeq
  19. 19. 3khz / MAP-004 update
  20. 20. Portability May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar
  21. 21. So, what happened in April? May Jun Aug Sep July Oct Nov Dec Jan Feb AprMar
  22. 22. Wish List What now? • Fast mode / more pores – Diagnostic & environmental metagenomics • Rapid sample prep • (very) Low input • Direct RNA sequencing MinION is unique: • Real-time • Portable • Super long reads
  23. 23. Acknowledgements Oxford Nanopore • Clive Brown • Zoe Macdougall • Daniel Turner • Stephanie Brooking • Oliver Hartwell • Gordon Sanghera • Spike Willcocks • Roger Pettett • Stodders • Apollo Steve • Bhupinder • ..and the entire team Dstl Porton Down • Simon Weller • Phil Rachwal • Jamie Taylor Heartlands Hospital • Peter Hawkey Public Health England • Phil Ashton • Tim Dallman GigaScience • Scott Edmunds University of Birmingham • Cathy Wardius • Szymon Calus Josh Quick

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