SPAdes swMATH ID: 17004 Software Authors: Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner Description: 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 (http://bioinf.spbau.ru/spades). It is distributed as open source software. Homepage: http://bioinf.spbau.ru/spades Related Software: Velvet; IDBA-UD; IDBA; ABySS; GAGE; MEGAHIT; SOAPdenovo; BLAT; Minimap2; FragGeneScan; Unicycler; Canu; SSAKE; ALLPATHS; QUAST; SEQuel; Prodigal; Mugsy; HHblits; Cd-hit Cited in: 17 Publications all top 5 Cited by 43 Authors 2 Cazaux, Bastien 2 Previtali, Marco 2 Puglisi, Simon J. 2 Radulescu, Andreea 2 Rivals, Eric 1 Alipanahi, Bahar 1 Bar-Joseph, Ziv 1 Belazzougui, Djamal 1 Bonizzoni, Paola 1 Boucher, Christina 1 Carugo, Oliviero 1 Chauve, Cedric 1 Chikhi, Rayan 1 Della Vedova, Gianluca 1 Eisenhaber, Frank 1 Faizrahnemoon, Mahsa 1 Gagie, Travis 1 Jean, Géraldine 1 Keith, Jonathan M. 1 Kolmogorov, Mikhail 1 Komusiewicz, Christian 1 Krishnamoorty, Sriram 1 Kulkarni, Milind Narayanrao 1 Lecroq, Thierry 1 Lee, Richard Chia-Tung 1 Lin, Yu 1 Lu, Chin Lung 1 Mäkinen, Veli 1 Mallawaarachchi, Vijini 1 Mane, Aniket C. 1 Medvedev, Paul 1 Muggli, Martin D. 1 Pirola, Yuri 1 Polevikov, Evgeny 1 Rizzi, Raffaella 1 Rusu, Irena 1 Sacomoto, Gustavo 1 Salmela, Leena 1 Schulz, Marcel H. 1 Shieh, Yi-Kung 1 Shyu, Shyong Jian 1 Tomescu, Alexandru Ioan 1 Wright, Christopher Cited in 5 Serials 2 Methods in Molecular Biology 1 Journal of Computer and System Sciences 1 Theoretical Computer Science 1 Algorithmica 1 International Journal of Foundations of Computer Science all top 5 Cited in 6 Fields 12 Biology and other natural sciences (92-XX) 8 Computer science (68-XX) 4 Combinatorics (05-XX) 1 General and overarching topics; collections (00-XX) 1 Statistics (62-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year