國家衛生研究院 NHRI:Item 3990099045/8595
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/8595


    Title: Completing bacterial genome assemblies: Strategy and performance comparisons
    Authors: Liao, YC;Lin, SH;Lin, HH
    Contributors: Division of Biostatistics and Bioinformatics
    Abstract: Determining the genomic sequences of microorganisms is the basis and prerequisite for understanding their biology and functional characterization. While the advent of low-cost, extremely high-throughput second-generation sequencing technologies and the parallel development of assembly algorithms have generated rapid and cost-effective genome assemblies, such assemblies are often unfinished, fragmented draft genomes as a result of short read lengths and long repeats present in multiple copies. Third-generation, PacBio sequencing technologies circumvented this problem by greatly increasing read length. Hybrid approaches including ALLPATHS-LG, PacBio corrected reads pipeline, SPAdes, and SSPACE-LongRead, and non-hybrid approaches-hierarchical genome-assembly process (HGAP) and PacBio corrected reads pipeline via self-correction-have therefore been proposed to utilize the PacBio long reads that can span many thousands of bases to facilitate the assembly of complete microbial genomes. However, standardized procedures that aim at evaluating and comparing these approaches are currently insufficient. To address the issue, we herein provide a comprehensive comparison by collecting datasets for the comparative assessment on the above-mentioned five assemblers. In addition to offering explicit and beneficial recommendations to practitioners, this study aims to aid in the design of a paradigm positioned to complete bacterial genome assembly.
    Date: 2015-03-04
    Relation: Scientific Reports. 2015 Mar 4;5:Article number 8747.
    Link to: http://dx.doi.org/10.1038/srep08747
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=2045-2322&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000350375900020
    Cited Times(Scopus): http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84929993004
    Appears in Collections:[Yu-Chieh Liao] Periodical Articles

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