Corporate Banner
Satellite Banner
Technology
Networks
Scientific Communities
 
Become a Member | Sign in
Home>Resources>White Papers>This White Paper
  White Papers
Scientific News
Shedding Light on HIV Vaccine Design
Broadly speaking - Mathematical modelling of host-pathogen coevolution sheds light on HIV vaccine design.
AACC 2016 Sees Clinical Chemistry Labs Drive Precision Medicine Offerings
Biomarker assays to enable precision medicine and risk assessment, mass spec-based tests designed for use in clinical labs large and small, and liquid biopsy technology captured the spotlight at the AACC annual meeting.
Automated Patch Clamping Trends
Learn more about current practices, preferences and metrics in ion channel drug screening using APC technology.
Lab-on-a-Stick: Miniaturised Clinical Testing For Fast Detection Of Antibiotic Resistance
A portable power-free test for the rapid detection of bacterial resistance to antibiotics has been developed by academics at Loughborough University and the University of Reading.
Genetic Ancestry of Cultivated Strawberry Unravelled
UNH scientists constructed a linkage map of the seven chromosomes of the diploid Fragaria iinumae, which allows them to fill in a piece of the genetic puzzle about the eight sets of chromosomes of the cultivated strawberry.
Progress In Vaccination Against Vespid Venom
Researchers at the Helmholtz Zentrum München and the Technical University Munich have presented a method which facilitates a personalised procedure for wasp allergy sufferers.
New Drug Target for Inflammatory Disorders
Penn study finds enigmatic molecules maintain equilibrium between fighting infection and inflammatory havoc.
Breast Cancer Cells Found To Switch Molecular Characteristics
Spontaneous interconversion between HER2-positive and HER2-negative states could contribute to progression, treatment resistance in breast cancer.
Mechanisms of Calcium Blockers
Researchers describe how the fundamental mode of action of two distinct chemical classes of calcium channel blockers differs.
Some Breast Cancer Patients With Low Genetic Risk Could Skip Chemotherapy
Genetic test can help predict survival and guide treatment options.
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
3,300+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,900+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!