Spades

SPAdes is a tool for assembling sequences from single-cell and multicell data types. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. It is better than E+V-SC for assembling single-cell data and Velvet and SoapDeNovo for assembling multicell data.

Topic

Sequence assembly

Detail

  • Operation: Genome assembly;Sequence assembly

  • Software interface: Command-line user interface

  • Language: Python

  • License: GPLv2

  • Cost: Free

  • Version name: 3.13.2

  • Credit: -

  • Input: -

  • Output: -

  • Contact: spades.support@cab.spbu.ru

  • Collection: -

  • Maturity: Mature

Publications

  • SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
  • Bankevich A, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. 2012; 19:455-77. doi: 10.1089/cmb.2012.0021
  • https://doi.org/10.1089/cmb.2012.0021
  • PMID: 22506599
  • PMC: PMC3342519

Download and documentation

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