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
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. https://doi.org/10.1093/bioinformatics/btr447
PMID: 21810899
PMCID: PMC3167058
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