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

Michael AlongeSebastian SoykSrividya RamakrishnanXingang WangSara GoodwinFritz J SedlazeckZachary B LippmanMichael C Schatz
Published in: Genome biology (2019)
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 .
Keyphrases
  • arabidopsis thaliana
  • copy number
  • genome wide
  • dna methylation
  • single cell
  • wastewater treatment
  • high resolution