University Library
  • Login
A gateway to Melbourne's research publications
Minerva Access is the University's Institutional Repository. It aims to collect, preserve, and showcase the intellectual output of staff and students of the University of Melbourne for a global audience.
View Item 
  • Minerva Access
  • Engineering
  • Computing and Information Systems
  • Computing and Information Systems - Research Publications
  • View Item
  • Minerva Access
  • Engineering
  • Computing and Information Systems
  • Computing and Information Systems - Research Publications
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

    A fast hybrid short read fragment assembly algorithm

    Thumbnail
    Citations
    Scopus
    Web of Science
    Altmetric
    36
    28
    Author
    Schmidt, B; Sinha, R; Beresford-Smith, B; Puglisi, SJ
    Date
    2009-09-01
    Source Title
    BIOINFORMATICS
    Publisher
    OXFORD UNIV PRESS
    University of Melbourne Author/s
    SINHA, RANJAN
    Affiliation
    Computer Science and Software Engineering
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Schmidt, B., Sinha, R., Beresford-Smith, B. & Puglisi, S. J. (2009). A fast hybrid short read fragment assembly algorithm. BIOINFORMATICS, 25 (17), pp.2279-2280. https://doi.org/10.1093/bioinformatics/btp374.
    Access Status
    This item is currently not available from this repository
    URI
    http://hdl.handle.net/11343/31774
    DOI
    10.1093/bioinformatics/btp374
    Abstract
    SUMMARY: The shorter and vastly more numerous reads produced by second-generation sequencing technologies require new tools that can assemble massive numbers of reads in reasonable time. Existing short-read assembly tools can be classified into two categories: greedy extension-based and graph-based. While the graph-based approaches are generally superior in terms of assembly quality, the computer resources required for building and storing a huge graph are very high. In this article, we present Taipan, an assembly algorithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources.
    Keywords
    Information Systems

    Export Reference in RIS Format     

    Endnote

    • Click on "Export Reference in RIS Format" and choose "open with... Endnote".

    Refworks

    • Click on "Export Reference in RIS Format". Login to Refworks, go to References => Import References


    Collections
    • Minerva Elements Records [45770]
    • Computing and Information Systems - Research Publications [1456]
    Minerva AccessDepositing Your Work (for University of Melbourne Staff and Students)NewsFAQs

    BrowseCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects
    My AccountLoginRegister
    StatisticsMost Popular ItemsStatistics by CountryMost Popular Authors