SSAKE is a de novo assembler for short DNA sequence reads. It is designed to help leverage the information from short sequences reads by assembling them into contigs and scaffolds that can be used to characterize novel sequencing targets. SSAKE is the first published algorithm for genome assembly with short DNA sequences. It assembles whole reads (not k-mers) and as such, is well-suited for structural variant assembly/detection. In 2016, SSAKE celebrates its 10th anniversary

References in zbMATH (referenced in 7 articles )

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  1. Comin, Matteo; Schimd, Michele: Assembly-free techniques for NGS data (2017)
  2. Jean, Géraldine; Radulescu, Andreea; Rusu, Irena: The contig assembly problem and its algorithmic solutions (2017)
  3. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  4. Nimmy, Sonia Farhana; Kamal, M. S.: Next generation sequencing under de novo genome assembly (2015)
  5. Jackson, Benjamin G.; Schnable, Patrick S.; Aluru, Srinivas: Parallel short sequence assembly of transcriptomes (2009) ioport
  6. Jr., Douglas W. Bryant; Wong, Weng-Keen; Mockler, Todd C.: QSRA - a quality-value guided \textitdenovoshort read assembler (2009) ioport
  7. Warren, René L.; Sutton, Granger G.; Jones, Steven J. M.; Holt, Robert A.: Assembling millions of short DNA sequences using ssake (2007) ioport