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 sequenc...

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Detalles Bibliográficos
Autores principales: Alonge, Michael, Soyk, Sebastian, Ramakrishnan, Srividya, Wang, Xingang, Goodwin, Sara, Sedlazeck, Fritz J., Lippman, Zachary B., Schatz, Michael C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816165/
https://www.ncbi.nlm.nih.gov/pubmed/31661016
http://dx.doi.org/10.1186/s13059-019-1829-6
Descripción
Sumario: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.

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