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SPAdes

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A. Background and Development 1. Origin and creators - Developed at St. Petersburg Academic University - Led by Pavel Pevzner's team 2. Initial release and purpose - First released in 2012 - Designed to address challenges in single-cell and short-read sequencing B. Key Features and Innovations 1. Versatility - Suitable for both single-cell and standard (multicell) assembly - Adaptable to various sequencing technologies 2. Core algorithmic innovations - Multisized de Bruijn graph approach - Advanced error correction tailored for different data types - Paired assembly graph for improved use of read-pair information 3. Specialized capabilities - Effective handling of uneven coverage (crucial for single-cell data) - Hybrid assembly combining short and long reads - Dedicated modes for metagenome, transcriptome, and plasmid assembly C. Impact and Adoption 1. Widespread use in genomics research 2. Continuous development and community support

  1. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., ... & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology, 19(5), 455-477. DOI: 10.1089/cmb.2012.0021 ↩

  2. Prjibelski, A. D., Vasilinetc, I., Bankevich, A., Gurevich, A., Krivosheeva, T., Nurk, S., ... & Pevzner, P. A. (2014). ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics, 30(12), i293-i301. DOI: 10.1093/bioinformatics/btu266 ↩