@article {82,
	title = {RaGOO: fast and accurate reference-guided scaffolding of draft genomes.},
	journal = {Genome Biol},
	volume = {20},
	year = {2019},
	month = {2019 Oct 28},
	pages = {224},
	abstract = {<p>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 .</p>},
	issn = {1474-760X},
	doi = {10.1186/s13059-019-1829-6},
	author = {Alonge, Michael and Soyk, Sebastian and Ramakrishnan, Srividya and Wang, Xingang and Goodwin, Sara and Sedlazeck, Fritz J and Lippman, Zachary B and Schatz, Michael C}
}
