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!

lex.nederbragt@bio.uio.no

www.sequencing.uio.no

www.sequencing.uio.no