Data handling strategies for high throughput pyrosequencers

Trombetti, Gabriele; Bonnal, Raoul Jean Pierre; Rizzi, Ermanno; Bellis, Gianluca De; Milanesi, Luciano

doi:10.1186/1471-2105-8-s1-s22

Cited by 23 publications

(11 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…288 One aspect that has not been mentioned in detail is the computing power required to handle and analyze longer and longer sequences involving more complex phylogenetic techniques. 289,290 The speed of processors seems not to be the limiting factor, per se, for all but the largest data sets. Rather it is the cost of acquiring such processing power, which may limit the ability of smaller research teams and institutions to perform such analyses, though there may be more strategic, analytical ways around this problem.…”

Section: Discussionmentioning

confidence: 97%

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Lam

Hon

Tang

2010

Critical Reviews in Clinical Laboratory Sciences

View full text Add to dashboard Cite

Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.

show abstract

Section: Discussionmentioning

confidence: 97%

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Lam

Hon

Tang

2010

Critical Reviews in Clinical Laboratory Sciences

View full text Add to dashboard Cite

show abstract

“…The VNAS framework has been used in various earlier and current projects besides the present one in order to raise the reliability and reduce the development time for new Grid applications such as [10,35]. A scheme of VNAS design is shown in Fig.…”

Section: The Hpc Layer and The Vnas Frameworkmentioning

confidence: 99%

Grid Based Genome Wide Studies on Atrial Flutter

et al. 2010

Self Cite

View full text Add to dashboard Cite

show abstract

“…This difficulty can be overcome by (1) using newer pyrosequencing technology, such as the Roche Titanium chemistry, that generates longer average read lengths and/or (2) obtaining greater sequencing depth. Moreover, the assembly of sequence data with a high number of repeated regions can be challenging due to contigs built based on repeated regions that can generate chimeric artifacts (Trombetti et al 2007). Microsatellites are relatively common markers throughout the genome of most species (Li et al 2002); thus, they can be efficiently isolated from genome sequencing of nonenriched (Abdelkrim et al 2009) and enriched libraries (Santana et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Discovery and characterization of microsatellites for the solitary bee Colletes inaequalis using Sanger and 454 pyrosequencing

et al. 2012

View full text Add to dashboard Cite

-The recent implementation of next-generation sequencing for the discovery of microsatellite markers has made this technology the most effective method for generating genetic markers in non-model organisms. Here, we report the de novo discovery of microsatellite markers for the solitary bee Colletes inaequalis using cloning/Sanger sequencing and direct 454 pyrosequencing from microsatellite-enriched genomic libraries. We identified and successfully multiplexed 18 highly variable microsatellite markers in 585 individuals. The number of alleles per locus ranged from 3 to 23, and the expected heterozygosity ranged from 0.056 to 0.912. These genetic markers will allow for the investigation of levels of inbreeding and fine-scale population structure in C. inaequalis. Our results contribute to the literature demonstrating that 454 sequencing is more time-and cost-efficient than cloning/Sanger sequencing at identifying a large number of genomic regions with microsatellite repeat motifs.SSRs / cloning / next-generation sequencing / Colletidae

show abstract

Data handling strategies for high throughput pyrosequencers

Cited by 23 publications

References 2 publications

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Grid Based Genome Wide Studies on Atrial Flutter

Discovery and characterization of microsatellites for the solitary bee Colletes inaequalis using Sanger and 454 pyrosequencing

Contact Info

Product

Resources

About