NEWS GENOME DATA ANALYSIS
Genome data analysis in hours
IMEC UNVEILS LATEST SOFTWARE PLATFORM FOR GENOME DATA ANALYSIS. NEIL TYLER REPORTS
Imec has unveiled the latest version of its software platform for DNA
analysis which is able to analyse samples eight to 16 times faster
than the genome analysis toolkit (GATK) - the widely-accepted standard
reference.
The elPrep5 platform encompasses the full analysis
pipeline from data preparation to variant calling on
a similar hardware infrastructure, opening up new
opportunities and ef ciency gains for hospitals
and medical practitioners.
“This is the breakthrough we have been
anticipating for years. Finally, we can run the
entire DNA analysis pipeline with a single
software platform solution, and faster than
ever,” said imec researcher Dr. Charlotte
Herzeel.
“Because variant calling is the most complex
step, gathering results up to 16 times faster than
the previous method has resulted in a four- to nine-fold
reduction in time, all while retaining GATK identical results.
“For the medical sector, this allows massive ef ciency gains
because the time between sampling and diagnosis dramatically
decreases and doctors can run analyses overnight. Moreover, since
many hospitals run their analyses via rented cloud solutions, the
reduced throughput times can immediately result in a cost reduction
per analysis.”
After a DNA sample is sequenced, there are hundreds of gigabytes
of data representing the genetic information of the original sample,
which, in the sequencing process, was cut into a multitude of smaller
fragments.
These fragments have to be reconstructed to a representation
of the original DNA sample. Afterwards, an analysis is then
performed to detect genetic variants, for example, in
comparison to a known reference model. elPrep 5 is
speci cally designed to optimise this variant calling
analysis.
Performing this analysis is a computationalheavy
challenge and despite substantial cost
reductions for DNA analysis over the past decade,
runtimes can still last up to two to three days for
a whole genome. imec’s elPrep5 can perform a
whole genome analysis within a few hours without
compromising the quality of the output.
By taking advantage of its parallel execution
framework, elPrep5 performs the complete analysis after
a single pass through the data. This architecture avoids the
intensive read and write processes of fragments of data in and out of
the memory.
elPrep5 is written in Go, an open-source programming language
developed by Google, and can be run on standard servers that most
hospitals have locally or in the cloud.
Several industrial partners have already expressed interest to
integrate elPrep5 into their daily operations.
The Internet of Trees for rapid wildfi re detection
Environmental IoT startup Dryad Networks
has secured funding of €1.8million to develop
a large-scale IoT network for the ultra-early
detection of wild res.
The company’s digital forest solution has
been designed to help public and private
forest owners monitor, analyse and protect
the world’s largest, most remote forests and
tackle the devastating impact of wild res on
the environment, wildlife and communities.
Dryad’s large-scale IoT solution uses a
network of sensors for ultra-early detection of
wild res in under 60 minutes even in remote
areas, prompting a faster response than
existing solutions.
By contrast, camera and satellite-based
solutions can take several hours or even
days to identify a re because they rely on
the smoke plume developing enough to be
detected from a long distance, while emerging
solutions based on the NarrowBand-Internet
of Things (NB-IoT) standard are not practical
for large-scale and remote forests where
the cost of building a LTE/4G network is
prohibitive.
Forest res account for around 20% of the
annual global emissions from the burning of
fossil fuel and account for the displacement
of tens of thousands of people, approximately
$5bn of direct re- ghting costs and over
$100bn of economic damage globally every
year.
The solution comprises of solar-powered
sensors that use AI to detect gases emitted
in the smouldering stage of a wild re as well
as temperature, humidity and air pressure;
gateways featuring Dryad’s patent-pending
distributed mesh architecture - an extension
to the LoRaWAN open standard for longrange
radio IoT networks and a cloud-based
dashboard to analyse and monitor a wide
range of indicators and alert forest managers.
Dryad’s gateways interconnect in
a multi-hop mesh network, making it
possible to cover very large forests,
rather than the real-world 12km range
supported by other LoRaWAN gateways
and makes it economically viable to build a
communications network for large forests
where there is no mobile network coverage.
Dryad border gateways at the edge of the
network connect to wireless (LTE/NB-IoT),
satellite or wired internet to access the Dryad
cloud platform.
Carsten Brinkschulte, CEO and co-founder
of Dryad Networks, said: “The notion of
the intelligent forest is now coming of
age. Our vision is to deliver an effective
communications architecture for even the
most remote forests and make sub one-hour
wild re detection the new reality. Using a
solar-powered, distributed mesh IoT network
capable of covering vast expanses of forest
where mobile network coverage is lacking will
radically transform the way forests can be
monitored and managed.”
8 13 October 2020 www.newelectronics.co.uk
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