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Probe selection for DNA microarrays using OligoWiz. In Nat Protoc, 2(11), pages 2677--2691, 2007."},{"key":"e_1_3_2_1_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti155"},{"key":"e_1_3_2_1_34_1","first-page":"821","volume-title":"Genome Research 18 (5)","author":"Zerbino D.","year":"2008","unstructured":"D. Zerbino and E. Birney . Velvet: Algorithms for de novo short read assembly using de Bruijn graphs . In Genome Research 18 (5) , pages 821 -- 829 , 2008 . D. Zerbino and E. Birney. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. 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