DNAnexus Enables Seamless Assembly of PacBio Data for J. Craig Venter Genome
March 02 2015 - 8:00AM
Business Wire
Cloud Platform Facilitates and Speeds Reference
Quality De Novo Whole Genome Sequencing
DNAnexus Inc., a pioneer in cloud-based genome informatics and
data management, today announced that it now offers whole genome
assembly using long read sequencing data generated by the PacBio RS
II. To demonstrate the new capability, DNAnexus and PacBio
researchers used Daligner written by Gene Myers and PacBio’s FALCON
genome assembler to perform de novo genome assembly of the complete
genome of J. Craig Venter, a pioneer in genome sequencing, on the
DNAnexus cloud platform.
The first human reference genome was published back in 2001, and
it was a multiyear effort with a price tag in the billions. Venter
is the first single individual reference genome, published in 2007.
DNAnexus and PacBio were able to create a higher resolution version
of his genome reference, capturing important structural variant
information, in a fraction of the original time and cost. More
details on this announcement can be found here.
De novo genome assembly is a data and compute intensive task.
Researchers performing de novo processing often find that their
local infrastructure does not have the available resources or
expertise necessary for the complex assemblies. The DNAnexus
platform gives scientists access to massive computational resources
on a cost-effective, on-demand basis and has packaged the FALCON
assembler in a way that can be run without complicated
installation.
The cost to assemble a genome depends on the genome size,
complexity, and chosen coverage. Human genome assembly at 50 - 80x
coverage can be completed in less than 48 hours and priced between
$5,000 and $10,000 on the DNAnexus platform. Democratizing
reference genomes via de novo assembly provides research labs of
all sizes the ability to create their own reference genomes,
lowering local cluster infrastructure requirements, and shortening
time to results.
The ability to create a novel de novo reference genome, whether
it be for more accurate remapping of human populations such as the
Asian Reference Genome Project, or for crops with no existing
reference, has the potential for advancing breakthroughs in
scientific discovery.
"The DNAnexus platform brings the capability to perform full de
novo assembly of complex genomes into the reach of more
scientists," said Michael Hunkapiller, Chief Executive Officer of
Pacific Biosciences. "It is essential to have full and accurate de
novo human genome assemblies to facilitate our understanding of
disease, and it’s terrific that the DNAnexus platform allows
researchers to leverage PacBio tools and massive datasets to
conduct these types of pioneering research projects in the
cloud."
During PacBio’s Friday lunchtime workshop at the 16th annual
Advances in Genome Biology and Technology, Dr. W. Richard McCombie
from Cold Spring Harbor Laboratory announced the fastest human
genome assembly in history was just completed that day on DNAnexus.
DNAnexus ran FALCON on a breast cancer genome cell line from MSKCC,
which completed in less than 21 hours. DNAnexus is in collaboration
with PacBio to develop new features and improve current PacBio
assembly technology in the cloud. FALCON, along with full datasets
of Drosophila, Arabidopsis, and CHM13, and MSKCC can be found on
the DNAnexus platform under "featured projects." Venter’s PacBio
data will become available pending publication.
"We are thrilled to support PacBio to further improve powerful
long-read technology," said Richard Daly, CEO, DNAnexus. "We are
seeing a growing presence and pace of PacBio adoption across
genomic centers worldwide and are proud that the DNAnexus platform
provides a high-speed data management solution for PacBio data and
tools."
About DNAnexus
DNAnexus provides a global network genomic data management to
accelerate genomic medicine. The DNAnexus cloud-based platform is
optimized to address the challenges of security, scalability, and
collaboration, for organizations that are pursuing genomic-based
approaches to health, in the clinic and in the research lab. The
DNAnexus team is made up of experts in computational biology and
cloud computing who work with organizations to tackle some of the
most exciting opportunities in human health, making it easier—and
in many cases feasible—to work with genomic data. With DNAnexus,
organizations can stay a step ahead in leveraging genomics to
achieve their goals. The future of human health is in genomics.
DNAnexus brings it all together. For more information please visit:
https://dnanexus.com or follow us on Twitter @dnanexus
About Pacific Biosciences
Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the
PacBio RS II DNA Sequencing System to help scientists solve
genetically complex problems. Based on its novel Single Molecule,
Real-Time (SMRT) technology, the company's products enable:
targeted sequencing to more comprehensively characterize genetic
variations; de novo genome assembly to more fully identify,
annotate, and decipher genomic structures; and DNA base
modification identification to help characterize epigenetic
regulation and DNA damage. By providing access to information that
was previously inaccessible, Pacific Biosciences enables scientists
to increase their understanding of biological systems. More
information is available at www.pacb.com.
Element Public Relations, for DNAnexusTim Smith,
415-350-3019tsmith@elementpr.comorBioscribe, for Pacific
BiosciencesNicole Litchfield, 415-793-6468nicole@bioscribe.com
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