SOAPdenovo

SOAPdenovo is a tool for de novo genome assembly using entirely Illumina short reads. The algorithm implements error correction, de Bruijn graph construction, tip removal, repeat resolution, bubbles merging, contig linkage graph and scaffolding. This tool has a modularized design for each assembly step and has been proven to work on human genomes.

Topic

Sequence assembly

Detail

  • Operation: Genome assembly; Scaffolding

  • Software interface: command-line user interface

  • Language: -

  • License: -

  • Cost: free

  • Version name: -

  • Credit: Chinese Academy of Science; National Natural Science Foundation of China; International Science and Technology Cooperation Project (0806); Shenzhen hundred-million project; Danish Platform for Integrative Biology; Danish Natural Science Research Council

  • Input: -

  • Output: -

  • Contact: soap@genomics.org.cn

  • Collection: -

  • Maturity: -

Publications

  • De novo assembly of human genomes with massively parallel short read sequencing.
  • Li R, et al. De novo assembly of human genomes with massively parallel short read sequencing. De novo assembly of human genomes with massively parallel short read sequencing. 2010; 20:265-72. doi: 10.1101/gr.097261.109
  • https://doi.org/10.1101/gr.097261.109
  • PMID: 20019144
  • PMC: PMC2813482

Download and documentation

    Currently not available or not maintained.

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