PadeNA: A parallel de novo assembler

Gaurav Thareja, Vivek Kumar, Mike Zyskowski, Simon Mercer, Bob Davidson

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Recent technological advances in DNA sequencing technology are resulting in ever-larger quantities of sequence information being made available to an increasingly broad segment of the scientific and clinical community. This is in turn driving the need for standard, rapid and easy to use tools for genomic reconstruction and analysis. As a step towards addressing this challenge, we present PadeNA (Parallel de Novo Assembler), a parallelized DNA sequence assembler with a graphical user interface. PadeNA is designed using interface-driven architecture to facilitate code reusability and extensibility, and is provided as part of the open source Microsoft Biology Foundation. Installers and documentation are available at http://research.microsoft.com/bio/ .

Original languageEnglish
Title of host publicationBIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms
Pages196-203
Number of pages8
Publication statusPublished - 15 Jul 2011
Externally publishedYes
EventInternational Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011 - Rome, Italy
Duration: 26 Jan 201129 Jan 2011

Other

OtherInternational Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011
CountryItaly
CityRome
Period26/1/1129/1/11

Fingerprint

DNA sequences
Reusability
Graphical user interfaces
Interfaces (computer)
DNA
DNA Sequencing
Graphical User Interface
DNA Sequence
Open Source
Biology
Genomics
Standards
Community
Architecture

Keywords

  • De bruijn graph
  • DNA sequence assembly
  • Genomics
  • Scaffold generation

ASJC Scopus subject areas

  • Information Systems
  • Applied Mathematics

Cite this

Thareja, G., Kumar, V., Zyskowski, M., Mercer, S., & Davidson, B. (2011). PadeNA: A parallel de novo assembler. In BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (pp. 196-203)

PadeNA : A parallel de novo assembler. / Thareja, Gaurav; Kumar, Vivek; Zyskowski, Mike; Mercer, Simon; Davidson, Bob.

BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. 2011. p. 196-203.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Thareja, G, Kumar, V, Zyskowski, M, Mercer, S & Davidson, B 2011, PadeNA: A parallel de novo assembler. in BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. pp. 196-203, International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011, Rome, Italy, 26/1/11.
Thareja G, Kumar V, Zyskowski M, Mercer S, Davidson B. PadeNA: A parallel de novo assembler. In BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. 2011. p. 196-203
Thareja, Gaurav ; Kumar, Vivek ; Zyskowski, Mike ; Mercer, Simon ; Davidson, Bob. / PadeNA : A parallel de novo assembler. BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. 2011. pp. 196-203
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