Because of the open nature of the BioRuby project, both BioRuby and BioGem software modules are increasingly used and cited in biomedical research, not only in genomics, but also in phylogenetics and prediction of protein structural complexes and data integration.
Chapter 9 presents sambamba, a software tool for scaling up next generation sequencing NGS alignment processing through the use of multiple cores on a computer. Sambamba is a replacement for samtools, a commonly used software tool for working with aligned output from sequencers. Sambamba makes use of multi-core processing and is written in the D programming language. Not only does sambamba outperform samtools, but it already comes with an improved deduplication routine and other facilities, such as easy filtering of data.
The Sambamba software is now used in the large sequencing centres around the world. The chapter discusses computational bottlenecks and proves prescient because the number of citations of this paper increases every year.
This includes improved scientific career tracks for bioinformaticians and dedicated funding for big data software development. Chapter 12 discusses the computational methods and software solutions presented in this thesis, painting a picture of further challenges in bioinformatics computational solutions for the elucidation of biological processes. The chapter starts with a discussion on the merits and shortcomings of each individual software solution presented in this thesis, followed by a perspective on next generation sequencing, data integration and future research in software solutions.
High-throughput open source computational methods for genetics and genomics.
Project : PhD. High-throughput open source computational methods for genetics and genomics J. Laboratory of Nematology. Abstract Biology is increasingly data driven by virtue of the development of high-throughput technologies, such as DNA and RNA sequencing. Fingerprint genomics.
Biological Sciences. Arabidopsis thaliana.source url
Globodera rostochiensis. Meloidogyne incognita. Keywords plant parasitic nematodes dna sequencing next generation sequencing throughput computational science genetics genomics. Wageningen: Wageningen University. Prins, J.
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Wageningen : Wageningen University, Prins JCP. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function of genomes of higher organisms, has generated, however, not only a huge and burgeoning body of data but also a new class of scientific questions.
The nature and complexity of these questions will require, beyond establishing a new kind of alliance between experimental and theoretical disciplines, also the development of new generations both in computer software and hardware technologies, respectively. Many of us still feel that computational models rationalizing experimental findings in genome research fulfil their promises more slowly than desired.
There also is an uncertainity concerning the real position of a 'theoretical genome research' in the network of established disciplines integrating their efforts in this field. Product Details Table of Contents.
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Lehrach et al. Durbin, UJ.
The Integrated Genomic Database O. Genetic Mapping J.
Slezak et al. Searching Protein Sequence Databases W. Herrmann, S. Statistical Models of Chromosome Evolution M.
Deciphering the Genetic Message C. Show More. Average Review. Write a Review.
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