Download - NGS: bioinformatic challenges
Next generation sequencing research opportunities and bioinformatic challenges
Lex NederbragtNorwegian High-Throughput Sequencing Centre (NSC)
andCentre 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
pathogenomics.bham.ac.uk/hts
Oslo: 5 instrumentsTromsø: 1 instrument
Norwegian Sequencing Center
454 GS FLX
Illumina HiSeq
Illumina GaIIx
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
wikimedia commons
A genome project in Norway!
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 softwarehard to judge if programs are
any goodsometimes a challenge to
install a program andget it working
http://neidetcher.com/ubuntu_package_dependency.html
Dependency hell
http://neidetcher.com/ubuntu_package_dependency.html
Dependency hell
http://neidetcher.com/ubuntu_package_dependency.html
http://en.wikipedia.org/wiki/Dependency_hell
Challenges
Cpu power/memory needs high for some applications
Challenges
New technologies coming soonNext-Next-Generation Sequencing
http://www.pacificbiosciences.com
NSC expectsdelivery of the
Pacific Biosciences RSin December 2011
Challenges
New instruments coming soon
Ion Torrent PGM Illumina MiSeq
Oxford NanoporeGridION
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
plotsheatmaps
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?
annotation?
comparative genomics?
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
galaxyhyperbrowser (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?(http://www.ifi.uio.no/research/clsi/)
linkedin.comifi.uio.no
Thank you!
www.sequencing.uio.no
www.sequencing.uio.no