Article
Hybrid assembly with long and short reads improves discovery of gene family expansions.
BMC genomics - 19 Jul 2017
Miller Jason R, Zhou Peng, Mudge Joann, Gurtowski James, Lee Hayan, Ramaraj Thiruvarangan, Walenz Brian P, Liu Junqi, Stupar Robert M, Denny Roxanne, Song Li, Singh Namrata, Maron Lyza G, McCouch Susan R, McCombie W Richard, Schatz Michael C, Tiffin Peter, Young Nevin D, Silverstein Kevin A T
Abstract excerpt
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude...
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