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Alonge, Michael; Soyk, Sebastian; Ramakrishnan, Srividya; Wang, Xingang; Goodwin, Sara; Sedlazeck, Fritz J; Lippman, Zachary B; Schatz, Michael C
Genome Biology, 10/2019, Letnik: 20, Številka: 1Journal Article
We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO .
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