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

TitleRaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Publication TypeJournal Article
Year of Publication2019
AuthorsAlonge, M, Soyk, S, Ramakrishnan, S, Wang, X, Goodwin, S, Sedlazeck, FJ, Lippman, ZB, Schatz, MC
JournalGenome Biol
Date Published2019 Oct 28
KeywordsArabidopsis, Genome, Plant, Genomic Structural Variation, Genomics, Software, Solanum lycopersicum

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 .

Alternate JournalGenome Biol
PubMed ID31661016
PubMed Central IDPMC6816165
Grant ListS10 OD020122 / OD / NIH HHS / United States
R01-HG006677 / NH / NIH HHS / United States
UM1 HG008898 / NH / NIH HHS / United States

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