國家衛生研究院 NHRI:Item 3990099045/7113
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/7113


    Title: CISA: Contig integrator for sequence assembly of bacterial benomes
    Authors: Lin, SH;Liao, YC
    Contributors: Division of Biostatistics and Bioinformatics
    Abstract: A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. However, few efforts have been pursued to take advantage of multiple assemblies to yield an assembly of high accuracy. In this study, we employ various state-of-the-art assemblers to generate different sets of contigs for bacterial genomes. A tool, named CISA, has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine.
    Date: 2013-03-28
    Relation: PLoS ONE. 2013 Mar 28;8(3):Article number e60843.
    Link to: http://dx.doi.org/10.1371/journal.pone.0060843
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=1932-6203&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000317262200132
    Cited Times(Scopus): http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84875546384
    Appears in Collections:[Yu-Chieh Liao] Periodical Articles

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