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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.


Sequence assembly



Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA "SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing." J Comput Biol. 2012 May;19(5):455-77. 16.
PMID: 22506599
PMCID: PMC3342519

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