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

• Main Authors: Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz J. Sedlazeck, Zachary B. Lippman, Michael C. Schatz
• Format: Article
• Language: English
• Published: BMC 2019-10-01
• Series: Genome Biology
• Subjects: Pseudomolecule; Reference-guided; Genome assembly; Scaffolding; Genome alignment; Long-read sequencing
• Online Access: http://link.springer.com/article/10.1186/s13059-019-1829-6

Abstract 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.