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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

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 NGS: bioinformatic challenges Presentation Transcript

  • Next generation sequencing research opportunities and bioinformatic challenges
    Lex Nederbragt
    Norwegian High-Throughput Sequencing Centre (NSC)
    and
    Centre for Ecological and Evolutionary Synthesis (CEES)
  • Found on twitter:
  • Sequencing cost
  • Doubling times
     http://genomebiology.com/2010/11/5/207
  • Democratization
    pathogenomics.bham.ac.uk/hts
  • Democratization
    Oslo: 5 instruments
    Tromsø: 1 instrument
    pathogenomics.bham.ac.uk/hts
  • Norwegian Sequencing Center
    IlluminaHiSeq
    IlluminaGaIIx
    454 GS FLX
  • Norwegian Sequencing Center
    more than 75 runs in 2010
    two thirds 454 GS FLX
    Users from Norway and abroad
    all possible applications
  • Research possibilities
    Affordable sequencing
    Accessible sequencing
  • Research possibilities
    A genome project in Norway!
    wikimedia commons
  • Research possibilities
    Soon:
    sequencing human genomes in Norway!
    Apologies to www.prism-magazine.org
  • But...
  • Challenge
    Low cost sequencing
    +
    Availability to every lab
    =
    Data deluge
  • 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/
  • Challenges
     http://genomebiology.com/2010/11/5/207
  • Challenges
    Constant stream of new software
    http://seqanswers.com/forums/showthread.php?t=43
  • Challenges
    Constant stream of new software
    • hard to judge if programs are
    any good
    • sometimes a challenge to
    install a program and
    get it working
    http://neidetcher.com/ubuntu_package_dependency.html
  • Dependency hell
    http://neidetcher.com/ubuntu_package_dependency.html
  • Dependency hell
    http://en.wikipedia.org/wiki/Dependency_hell
    http://neidetcher.com/ubuntu_package_dependency.html
  • Challenges
    Cpu power/memory needs high for some applications
  • Challenges
    New technologies coming soon
    Next-Next-Generation Sequencing
    NSC expects
    delivery of the
    Pacific Biosciences RS
    in December 2011
    http://www.pacificbiosciences.com
  • Challenges
    New instruments coming soon
    Oxford Nanopore
    GridION
    Ion Torrent PGM
    IlluminaMiSeq
  • Challenges
    New technologies coming soon
    New data formats
    New types of experiments
    New types of analyses
  • Lessons from the cod project
    Steep learning curve
    wikipedia.org
  • Lessons from the cod project
    Learn unix
    wikipedia.org
  • Lessons from the cod project
    Do not underestimate the bioinformatics
    Buying sufficient compute power saved us
  • Lessons from the cod project
    'Hiring' people for specific tasks can help
  • Lessons from the cod project
    It is possible!
    34 tables, 23 figures, 78 pages supplementary
    http://www.wordle.net
  • Cod project bioinformatics
    plots heatmaps
  • Cod project bioinformatics
    combined plots
  • Cod project bioinformatics
    We learned a lot!
    but...
  • Cod project bioinformatics
    How many times did we reinvent the wheel?
    blogs.technet.com
  • Norwegian Sequencing Center
    Just a data provider?
    www.sequencing.uio.no
  • Norwegian Sequencing Center
    User gets stuck with analysis
    =
    No paper
    =
    Waste of resources
  • Norwegian Sequencing Center
    User:
    "I have the hypothesis"
    "You gave me the data"
    "I need help to answer my question"
  • 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
  • NSC bioinformaticians
    should NSC test these programs?
    should NSC/UiO provide computing power?
    does NSC have a responsibility to provide
    infrastructure?
    applications?
    training?
    analyses?
  • NSC bioinformaticians
    if we do analyses:
    as collaboration, i.e. coauthor?
    charge per hour?
    are Norwegian researchers used to collaborate in this way?
  • NSC bioinformaticians
    where does analysis stop?
    assembly?
    comparative genomics?
    annotation?
  • Example: CEES
    More and more NGS projects
    Too few bioinformaticians
  • Solutions
    Training
    Courses
  • Solutions
    Funds for bioinformaticians
    http://www.dinside.no
  • Solutions
    web-based programs
  • Galaxy
    usegalaxy.org
  • Hyperbrowser
    hyperbrowser.uio.no
  • Solutions
    web-based programs
    galaxy
    hyperbrowser (UiO!)
    Can NSC contribute to the development of these?
  • Solutions
    File standards
    coming
    SAM
    BAM
    BED
    WIG
    ...
    Can NSC/UiO contribute to the development of these standards?
    samtools.sourceforge.net
  • Solutions
    FUGE bioinformatics platform
    bioinfo.no
  • Solutions
    Computational Life Science initiative?
    linkedin.com
    ifi.uio.no