SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. The lion’s share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( It is distributed as open source software.

References in zbMATH (referenced in 12 articles )

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  1. Cazaux, Bastien; Lecroq, Thierry; Rivals, Eric: Linking indexing data structures to de Bruijn graphs: construction and update (2019)
  2. Wright, Christopher; Krishnamoorty, Sriram; Kulkarni, Milind: MULKSG: \textitMULtiple\textitK\textitSimultaneous\textitGraphassembly (2019)
  3. Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.: Bidirectional variable-order de Bruijn graphs (2018)
  4. Alipanahi, Bahar; Salmela, Leena; Puglisi, Simon J.; Muggli, Martin; Boucher, Christina: Disentangled long-read de Bruijn graphs via optical maps (2017)
  5. Bonizzoni, Paola; Della Vedova, Gianluca; Pirola, Yuri; Previtali, Marco; Rizzi, Raffaella: An external-memory algorithm for string graph construction (2017)
  6. Jean, Géraldine; Radulescu, Andreea; Rusu, Irena: The contig assembly problem and its algorithmic solutions (2017)
  7. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  8. Schulz, Marcel H.; Bar-Joseph, Ziv: Probabilistic models for error correction of nonuniform sequencing data (2017)
  9. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  10. Cazaux, Bastien; Sacomoto, Gustavo; Rivals, Eric: Superstring graph: a new approach for genome assembly (2016)
  11. Tomescu, Alexandru I.; Medvedev, Paul: Safe and complete contig assembly via omnitigs (2016)
  12. Komusiewicz, Christian; Radulescu, Andreea: On the sound covering cycle problem in paired de Bruijn graphs (2015)