RaGOO: fast and accurate reference-guided scaffolding of draft genomes

Published on Oct 28, 2019in Genome Biology13.583
路 DOI :10.1186/S13059-019-1829-6
Michael Alonge10
Estimated H-index: 10
(Johns Hopkins University),
Sebastian Soyk12
Estimated H-index: 12
(CSHL: Cold Spring Harbor Laboratory)
+ 5 AuthorsMichael C. Schatz73
Estimated H-index: 73
(Johns Hopkins University)
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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