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

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…

• NS
  National Science Foundation

  Awards: MCB180087, 1732253, 1445025, DBI-1350041, IOS-1445025, R01-HG006677, 1350041, IOS-1732253
• NI
  National Institutes of Health

  Awards: R01-HG006677, HG006677, UM1 HG008898