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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.


Sequence assembly


  • Operation: Genome assembly; Scaffolding
  • Software interface: command-line user interface
  • Language: -
  • Operating system: Linux
  • License: Not stated
  • 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
  • Contact: soap _at_
  • Collection: -


Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J "De novo assembly of human genomes with massively parallel short read sequencing." Genome Res. 2010; 20(2):265-72
PMID: 20019144
PMCID: PMC2813482

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