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1 Next Gen Bioinformatics 1718
1 Next Gen Bioinformatics 1718
SEQUENCING AND
BIOINFORMATICS
Moore's law: the number of transistors in a dense integrated
circuit doubles every two years
Moore's law calculates and predicts the pace of
improvement of one of the fastest improving
technologies, computers
In the last 15 years the pace of improvement of DNA
sequencing technologies has been much faster than that
of computers
Frederick Sanger
Nobel prize in chemistry in 1958 for sequencing insulin (and
proteins in general)
• Roche/454 FLX
• IonTorrent
NEXT-GENERATION DNA SEQUENCING
MAIN CHARACTERISTICS
EXTREME MINIATURIZATION
MASSIVE PARALLELIZATION
EXTREME MINIATURIZATION
MASSIVE PARALLELIZATION
ROCHE/454 GSFLX+
OUTPUT:
Generates reads up to 1,000
nucleotides long
sequencing by synthesis
ILLUMINA/SOLEXA
• Shorter reads
blocking the incorporation of multiple nucleotides is one of
the basis of the Illumina method
Each cycle imperfect blocking happens, a small percentage
of the copies in a cluster incorporates two nucleotides,
giving noise instead of good signal
When this percentage reaches a threshold, the signal is lost
An instrument: $ 60,000
A run: ~ $ 1,000 (high scalability)
• Pacific Biosciences
• Oxford Nanopore
THIRD GENERATION
SEQUENCING TECHNOLOGIES
REAL TIME SEQUENCING
Advantage
THIRD GENERATION
SEQUENCING TECHNOLOGIES
REAL TIME SEQUENCING
Advantage
http://flxlexblog.wordpress.com/2013/10/01/developments-in-next-generation-sequencing-october-2013-edition/
NEXT-GEN IS TRENDY
4. Data Analysis
What is your goal?
What exactly is the problem you want to address?
Evaluate approaches used in the past
Consider new approaches
Consider future problems
NO WAY BACK!
CHOOSE THE RIGHT TECHNOLOGY
This is HIGH-THROUGHPUT!
HIGH-TROUGHPUT TECHNOLOGIES
Modelling
Shotgun proteomics
Network analysis
Structural biology
Machine learning
HIGH-TROUGHPUT TECHNOLOGIES
Next-generation sequencing
BIOINFORMATICS
Bioinformatics is the development and use of computer
methods for the analysis of biological data
Expensive
UNIX → LINUX
Why Linux?
Free and runs on most hardware
fully customizable
more efficient and stable
ABSOLUTELY NO
This is very friendly for us, but very far from the
‘machine language’
language
BUT
cd Folder1