NGS: bioinformatic challenges


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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

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  • Yes, it is true that I poorly understand what I am doing, but I am a molecular biologist and I don't have degree in bioinformatics/statistics/or any computer related field. I don't want to describe here my situation with my supervisor, I have now two ways out from my situation - give up on my PhD or do everything I can do to finish.My supervisor doesn't want to collaborate with anyone, he says that "this is easy". Instead of getting to the end of my PhD I find myself fighting with my supervisor and seeking for help on forum. All I dream of is to finish and find a job within a group doing 'real' metagenomics. But, without any publications I don't have chance to obtain that.
  • NGS: bioinformatic challenges

    1. 1. Next generation sequencing research opportunities and bioinformatic challenges<br />Lex Nederbragt<br />Norwegian High-Throughput Sequencing Centre (NSC)<br />and<br />Centre for Ecological and Evolutionary Synthesis (CEES)<br />
    2. 2. Found on twitter:<br />
    3. 3. Sequencing cost<br />
    4. 4. Doubling times<br /><br />
    5. 5. Democratization<br /><br />
    6. 6. Democratization<br />Oslo: 5 instruments<br />Tromsø: 1 instrument<br /><br />
    7. 7. Norwegian Sequencing Center<br />IlluminaHiSeq<br />IlluminaGaIIx<br />454 GS FLX<br />
    8. 8. Norwegian Sequencing Center<br />more than 75 runs in 2010<br />two thirds 454 GS FLX<br />Users from Norway and abroad<br />all possible applications<br />
    9. 9. Research possibilities<br />Affordable sequencing<br />Accessible sequencing<br />
    10. 10. Research possibilities<br />A genome project in Norway!<br />wikimedia commons<br />
    11. 11. Research possibilities<br />Soon: <br />sequencing human genomes in Norway!<br />Apologies to<br />
    12. 12. But...<br />
    13. 13. Challenge<br />Low cost sequencing<br />+<br />Availability to every lab<br />=<br />Data deluge<br />
    14. 14. Challenges<br />"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."<br /><br />
    15. 15. Challenges<br /><br />
    16. 16. Challenges<br />Constant stream of new software<br /><br />
    17. 17. Challenges<br />Constant stream of new software<br /><ul><li>hard to judge if programs are </li></ul> any good<br /><ul><li>sometimes a challenge to</li></ul> install a program and<br /> get it working<br /><br />
    18. 18. Dependency hell<br /><br />
    19. 19. Dependency hell<br /><br /><br />
    20. 20. Challenges<br />Cpu power/memory needs high for some applications<br />
    21. 21. Challenges<br />New technologies coming soon<br />Next-Next-Generation Sequencing<br />NSC expects<br />delivery of the<br />Pacific Biosciences RS<br />in December 2011<br /><br />
    22. 22. Challenges<br />New instruments coming soon<br />Oxford Nanopore<br />GridION<br />Ion Torrent PGM<br />IlluminaMiSeq<br />
    23. 23. Challenges<br />New technologies coming soon<br />New data formats<br />New types of experiments<br />New types of analyses<br />
    24. 24. Lessons from the cod project<br />Steep learning curve<br /><br />
    25. 25. Lessons from the cod project<br />Learn unix<br /><br />
    26. 26. Lessons from the cod project<br />Do not underestimate the bioinformatics<br />Buying sufficient compute power saved us<br />
    27. 27. Lessons from the cod project<br />'Hiring' people for specific tasks can help<br />
    28. 28. Lessons from the cod project<br />It is possible!<br />34 tables, 23 figures, 78 pages supplementary<br /><br />
    29. 29. Cod project bioinformatics<br /> plots heatmaps<br />
    30. 30. Cod project bioinformatics<br />combined plots <br />
    31. 31. Cod project bioinformatics<br />We learned a lot!<br />but...<br />
    32. 32. Cod project bioinformatics<br />How many times did we reinvent the wheel?<br /><br />
    33. 33. Norwegian Sequencing Center<br />Just a data provider?<br /><br />
    34. 34. Norwegian Sequencing Center<br />User gets stuck with analysis<br />=<br />No paper<br />=<br />Waste of resources<br />
    35. 35. Norwegian Sequencing Center<br />User:<br />"I have the hypothesis"<br />"You gave me the data"<br />"I need help to answer my question"<br />
    36. 36. NSC user<br />user comfortable with data amounts, type, software?<br />should user learn unix?<br />should user buy commercial programs?<br />are these good enough?<br />should user go into cloud computing?<br /><br />
    37. 37. NSC bioinformaticians<br />should NSC test these programs?<br />should NSC/UiO provide computing power?<br />does NSC have a responsibility to provide<br />infrastructure?<br />applications?<br />training?<br />analyses?<br />
    38. 38. NSC bioinformaticians<br />if we do analyses:<br />as collaboration, i.e. coauthor?<br />charge per hour?<br />are Norwegian researchers used to collaborate in this way?<br />
    39. 39. NSC bioinformaticians<br />where does analysis stop?<br />assembly?<br />comparative genomics?<br />annotation?<br />
    40. 40. Example: CEES<br />More and more NGS projects<br />Too few bioinformaticians<br />
    41. 41. Solutions<br />Training<br />Courses<br />
    42. 42. Solutions<br />Funds for bioinformaticians<br /><br />
    43. 43. Solutions<br />web-based programs<br />
    44. 44. Galaxy<br /><br />
    45. 45. Hyperbrowser<br /><br />
    46. 46. Solutions<br />web-based programs<br />galaxy<br />hyperbrowser (UiO!)<br />Can NSC contribute to the development of these?<br />
    47. 47. Solutions<br />File standards<br />coming<br />SAM<br />BAM<br />BED<br />WIG<br />...<br />Can NSC/UiO contribute to the development of these standards?<br /><br />
    48. 48. Solutions<br />FUGE bioinformatics platform<br /><br />
    49. 49. Solutions<br />Computational Life Science initiative?<br /><br /><br />