Next generation sequencing: research opportunities and bioinformatic challenges. A seminar I gave for the Computational Life Science (Univ. of Oslo) seminar series, March 2, 2011

1. Next generation sequencing research opportunities and bioinformatic challenges Lex Nederbragt Norwegian High-Throughput Sequencing Centre (NSC) and Centre for Ecological and Evolutionary Synthesis (CEES)

2. Found on twitter:

3. Sequencing cost

4. Doubling times http://genomebiology.com/2010/11/5/207

5. Democratization pathogenomics.bham.ac.uk/hts

6. Democratization Oslo: 5 instruments Tromsø: 1 instrument pathogenomics.bham.ac.uk/hts

7. Norwegian Sequencing Center IlluminaHiSeq IlluminaGaIIx 454 GS FLX

8. Norwegian Sequencing Center more than 75 runs in 2010 two thirds 454 GS FLX Users from Norway and abroad all possible applications

9. Research possibilities Affordable sequencing Accessible sequencing

10. Research possibilities A genome project in Norway! wikimedia commons

11. Research possibilities Soon: sequencing human genomes in Norway! Apologies to www.prism-magazine.org

12. But...

13. Challenge Low cost sequencing + Availability to every lab = Data deluge

14. Challenges "The rule of thumb in the genomics community is that every dollar spent on sequencing hardware must be matched by a comparable investment in informatics." http://www.the-scientist.com/2011/3/1/60/1/

15. Challenges http://genomebiology.com/2010/11/5/207

16. Challenges Constant stream of new software http://seqanswers.com/forums/showthread.php?t=43

18. Dependency hell http://neidetcher.com/ubuntu_package_dependency.html

19. Dependency hell http://en.wikipedia.org/wiki/Dependency_hell http://neidetcher.com/ubuntu_package_dependency.html

20. Challenges Cpu power/memory needs high for some applications

21. Challenges New technologies coming soon Next-Next-Generation Sequencing NSC expects delivery of the Pacific Biosciences RS in December 2011 http://www.pacificbiosciences.com

22. Challenges New instruments coming soon Oxford Nanopore GridION Ion Torrent PGM IlluminaMiSeq

23. Challenges New technologies coming soon New data formats New types of experiments New types of analyses

24. Lessons from the cod project Steep learning curve wikipedia.org

25. Lessons from the cod project Learn unix wikipedia.org

26. Lessons from the cod project Do not underestimate the bioinformatics Buying sufficient compute power saved us

27. Lessons from the cod project 'Hiring' people for specific tasks can help

28. Lessons from the cod project It is possible! 34 tables, 23 figures, 78 pages supplementary http://www.wordle.net

29. Cod project bioinformatics plots heatmaps

30. Cod project bioinformatics combined plots

31. Cod project bioinformatics We learned a lot! but...

32. Cod project bioinformatics How many times did we reinvent the wheel? blogs.technet.com

33. Norwegian Sequencing Center Just a data provider? www.sequencing.uio.no

34. Norwegian Sequencing Center User gets stuck with analysis = No paper = Waste of resources

35. Norwegian Sequencing Center User: "I have the hypothesis" "You gave me the data" "I need help to answer my question"

36. NSC user user comfortable with data amounts, type, software? should user learn unix? should user buy commercial programs? are these good enough? should user go into cloud computing? fsteurope.com

37. NSC bioinformaticians should NSC test these programs? should NSC/UiO provide computing power? does NSC have a responsibility to provide infrastructure? applications? training? analyses?

38. NSC bioinformaticians if we do analyses: as collaboration, i.e. coauthor? charge per hour? are Norwegian researchers used to collaborate in this way?

39. NSC bioinformaticians where does analysis stop? assembly? comparative genomics? annotation?

40. Example: CEES More and more NGS projects Too few bioinformaticians

41. Solutions Training Courses

42. Solutions Funds for bioinformaticians http://www.dinside.no

43. Solutions web-based programs

44. Galaxy usegalaxy.org

45. Hyperbrowser hyperbrowser.uio.no

46. Solutions web-based programs galaxy hyperbrowser (UiO!) Can NSC contribute to the development of these?

47. Solutions File standards coming SAM BAM BED WIG ... Can NSC/UiO contribute to the development of these standards? samtools.sourceforge.net

48. Solutions FUGE bioinformatics platform bioinfo.no

49. Solutions Computational Life Science initiative? (http://www.ifi.uio.no/research/clsi/) linkedin.com ifi.uio.no

50. Thank you! lex.nederbragt@bio.uio.no www.sequencing.uio.no www.sequencing.uio.no