Corporate Banner
Satellite Banner
Technology
Networks
Scientific Communities
 
Become a Member | Sign in
Home>Resources>White Papers>This White Paper
  White Papers
Scientific News
Flowering Regulation Mechanism Discovered
Monash researchers have discovered a new mechanism that enables plants to regulate their flowering in response to raised temperatures.
Turning Skin Cells into Heart, Brain Cells
In a major breakthrough, scientists at the Gladstone Institutes transformed skin cells into heart cells and brain cells using a combination of chemicals.
Nanoparticles Present Sustainable Way to Grow Food Crops
Nanoparticle technology can help reduce the need for fertilizer, creating a more sustainable way to grow crops such as mung beans.
How Scientists Use DNA to Track Disease Outbreaks
They’re the top questions on everyone’s mind when a new disease outbreak happens: where did the virus come from? When did this happen? How long has it been spreading in a particular country or group of people?
Genetic Risk Factors of Disparate Diseases Share Similar Biological Underpinnings
Penn Institute for Biomedical Informatics and colleagues identify "roadmap" of disease mechanisms to identify candidate drug targets.
Drugs that May Combat Deadly Antibiotic-Resistant Bacteria Uncovered
Study identifies 79 compounds that inhibit carbapenem-resistant Enterobacteriaceae (CRE).
Stem Cells Know How to Unwind
Research led by the Babraham Institute with collaborators in the UK, Canada and Japan has revealed a new understanding of how an open genome structure supports the long-term and unrestricted developmental potential in embryonic stem cells.
HIV Particles Used to Trap Intact Mammalian Protein Complexes
Belgian scientists from VIB and UGent developed Virotrap, a viral particle sorting approach for purifying protein complexes under native conditions.
Childhood Asthma Research Receives $2M
Research into the impact of a child’s upbringing and social and physical environments on the development of asthma will receive $2 million to tackle the condition that affects as many as one in three Canadians.
Growing Stem Cells More Safely
Nurturing stem cells atop a bed of mouse cells works well, but is a non-starter for transplants to patients – Brown University scientists are developing a synthetic bed instead.
Scroll Up
Scroll Down

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


CLC Bio

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
3,000+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,500+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!