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SEED is a tool clustering similar sequences prior to subsequent steps in genome assembly. It implements a modified space seed method known as block spaced seeds to efficiently cluster 100 million short reads in less than 4 hours and has linear time and memory performance.


Sequence assembly


  • Operation: Sequence clustering
  • Input: FASTQ
  • Output: -
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: -
  • Version name: -
  • Credit: Institute for Integrative Genome Biology
  • Contact: thomas.girke _at_
  • Collection: -


Bao E, Jiang T, Kaloshian I, Girke T "SEED: efficient clustering of next-generation sequences." Bioinformatics. 2011 Sep 15;27(18):2502-9. Epub 2011 Aug 2.
PMID: 21810899
PMCID: PMC3167058

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