Simplifier

Simplifier is a stand-alone software tool that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. It reduces the number of contigs generated by ab initio methods and increases the N50, thus reducing the effort required for finalization of genome assembly. Simplifier has been tested on data from prokaryotic organisms, including the genome of Corynebacterium pseudotuberculosis strain 258 and Escherichia coli DH10B, and has successfully reduced the number of contigs and the mate-paired library and fragment library.

Topic

Sequencing;DNA;Genomics;Sequence assembly

Detail

  • Operation: Sequence redundancy removal

  • Software interface: Command-line user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Fundação de Amparo a Pesquisa doEstado do Pará and Pronex Núcleo Amazônico de Excelênciaem Genômica de Microorganismos, Conselho Nacional deDesenvolvimento Científico e Tecnológico (CNPq), the Coordenação deAperfeiçoamento de Pessoal de Nível Superior (CAPES).

  • Input: -

  • Output: -

  • Contact: rommelramos@ufpa.br;asilva@ufpa.br

  • Collection: -

  • Maturity: -

Publications

  • Simplifier: a web tool to eliminate redundant NGS contigs.
  • Ramos RT, et al. Simplifier: a web tool to eliminate redundant NGS contigs. Simplifier: a web tool to eliminate redundant NGS contigs. 2012; 8:996-9. doi: 10.6026/97320630008996
  • https://doi.org/10.6026/97320630008996
  • PMID: 23275695
  • PMC: PMC3524941

Download and documentation

    Currently not available or not maintained.

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