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wtdbg2 is long-read based assembler that is 2 to 17 times faster than some published tools (as of 2020) that performed the same task. The algorithm basically follows the overlap-layout-consensus method but advanced it with a fast all-versus-all read alignment process. It also uses fuzzy-Bruijn graph.


Sequence assembly


  • Operation: Sequence assembly; De-novo assembly
  • Input: FASTA
  • Output: FASTA
  • Software interface: Command-line interface
  • Language: C
  • Operating system: Linux, Mac OS X
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 2.5
  • Credit: Natural Science Foundation of China, US National Institutes for Health
  • Contact: ruanjue _at_
  • Collection: -


Ruan J, Li H "Fast and accurate long-read assembly with wtdbg2." Nat Methods, 2020
PMID: 31819265
PMCID: PMC7004874

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