Related Experiment Video
Updated: Jan 4, 2026

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
Published on: August 18, 2023
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Michael Alonge1, Sebastian Soyk2, Srividya Ramakrishnan1
1Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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 .
Related Concept Videos
Genome Annotation and Assembly
Sanger Sequencing
Evolutionary Relationships through Genome Comparisons

