Corporate Banner
Satellite Banner
Scientific Communities
Become a Member | Sign in
Home>Resources>White Papers>This White Paper
  White Papers
Scientific News
Breaking Through the Barriers to Lab Innovation
Here we examine the drivers behind the move for greater innovation, the challenges and current trends in laboratory informatics, and the tools that can be used to break these barriers.
Education and Expense: The Barriers to Mass Spectrometry in Clinical Laboratories?
Here we examine the perceived barriers to mass spec in clinical laboratories and explore the possible drivers behind the recent shift in uptake of the technology in clinical settings.
Fruit Fly Pheromone Flags Great Real Estate for Starting a Family
Finding could aid efforts to control mosquito-borne diseases like malaria by manipulating odorants
Gene Editing Could Enable Pig-To-Human Organ Transplant
The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them.
Antioxidants Cause Malignant Melanoma to Metastasize Faster
Fresh research at Sahlgrenska Academy has found that antioxidants can double the rate of melanoma metastasis in mice.
New Therapy Reduces Symptoms of Inherited Enzyme Deficiency
A phase three clinical trial of a new enzyme replacement medication, sebelipase alfa, showed a reduction in multiple disease-related symptoms in children and adults with lysosomal acid lipase deficiency, an inherited enzyme deficiency that can result in scarring of the liver and high cholesterol.
Adult High Blood Pressure Risk Identifiable in Childhood
Groups of people at risk of having high blood pressure and other related health issues by age 38 can be identified in childhood, new University of Otago research suggests.
Analyzing Protein Structures in Their Native Environment
Enhanced-sensitivity NMR could reveal new clues to how proteins fold.
Supercoiled DNA is Far More Dynamic Than the “Watson-Crick” Double Helix
Researchers have imaged in unprecedented detail the three-dimensional structure of supercoiled DNA, revealing that its shape is much more dynamic than the well-known double helix.
Mini-kidneys Successfully Grown from Stem Cells
Researchers from Murdoch Childrens Research Institute have perfected a method of turning stem cells into mini-kidneys for use in drug screening, disease modelling and cell therapy.
Scroll Up
Scroll Down

White paper on de novo assembly in CLC Assembly Cell 3.0
Bookmark and Share


CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data. The command-line interface of CLC Assembly Cell enables the functionalities to be easily included in scripts and other Next Generation Sequencing work-flows.

CLC Assembly Cell is utilizing SIMD instructions to parallelize and accelerate the assembly algorithms, making the program the fastest Next Generation Sequencing assembler at present.

This is a white paper on the de novo assembler in CLC Assembly Cell 3.0. Note that the same algorithm is used by CLC Genomics Workbench and CLC Genomics Server, so except for the performance benchmarks (speed and memory), this white paper applies to these products as well after next release.

The assembler is designed to combine a mix of data from Illumina, 454, SOLiD and Sanger sequencing, both as single and as paired-end reads. For paired-end data, different insert sizes can be combined in the same assembly. Note that in the current version, paired-end SOLiD data can be used in a post-processing step to link contigs together.

This white paper consists of three parts: The first part explains how the assembler works, and the next focuses on large genome assembly of a human data set, where we have compared our assembler with the ABySS assembler which is also capable of assembling human genome-size data sets [Simpson et al., 2009]. The third part reports the results of a smaller bacterial data set where focus is on quality and where we have compared the quality and performance of our own assembly with one of the popular open source assembly algorithms, Velvet [Zerbino and Birney, 2008].

Further Information

Related Content

IBM and CLC bio Deliver Combined Turnkey Genomics Sequencing Analytics Solution
At the Bio-IT World conference in Boston, IBM and CLC bio announced a combined turnkey next generation sequencing data analytics solution.
Wednesday, April 10, 2013
CLC bio Acquires the Drug Discovery-software Company Molegro
The acquisition of Molegro supports CLC bio's strategy of continuously expanding their bioinformatics offerings beyond Next Generation Sequencing, as well as in bioinformatics areas of value to their customer base.
Monday, September 03, 2012
Convey Teams With CLC bio to Provide Exceptional Genomics Analysis
Deployed at the Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany, the new Convey-CLC bio solution substantially accelerates and extends HZI's ability to manage and analyze next generation sequencing (NGS) data.
Friday, April 20, 2012
CLC bio and VIB Agree on an Academic Regional Site License
Companies announced the signing of the site license agreement for CLC bio's sequence analysis software CLC DNA Workbench.
Thursday, February 09, 2012
Sapphire Energy Installs Custom-Made Software from CLC bio for Biofuel Research
Sapphire Energy has the potential to radically change the world's energy landscape with 'Green Crude' - a renewable crude oil that is a result of a proprietary process of turning sunlight, CO2, and algae into green oils to be refined into fuel.
Thursday, December 15, 2011
CLC bio Tests Next Generation Sequencing Solution on African Tuberculosis Data
CLC bio has joined forces with Inqaba Biotechnical Industries in an effort to help fight tuberculosis on the African continent.
Wednesday, February 13, 2008
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,700+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,800+ scientific videos