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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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
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author Alonge, Michael
Soyk, Sebastian
Ramakrishnan, Srividya
Wang, Xingang
Goodwin, Sara
Sedlazeck, Fritz J.
Lippman, Zachary B.
Schatz, Michael C.
author_facet Alonge, Michael
Soyk, Sebastian
Ramakrishnan, Srividya
Wang, Xingang
Goodwin, Sara
Sedlazeck, Fritz J.
Lippman, Zachary B.
Schatz, Michael C.
author_sort Alonge, Michael
collection PubMed
description 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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spelling pubmed-68161652019-10-31 RaGOO: fast and accurate reference-guided scaffolding of draft genomes Alonge, Michael Soyk, Sebastian Ramakrishnan, Srividya Wang, Xingang Goodwin, Sara Sedlazeck, Fritz J. Lippman, Zachary B. Schatz, Michael C. Genome Biol Method 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. BioMed Central 2019-10-28 /pmc/articles/PMC6816165/ /pubmed/31661016 http://dx.doi.org/10.1186/s13059-019-1829-6 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Alonge, Michael
Soyk, Sebastian
Ramakrishnan, Srividya
Wang, Xingang
Goodwin, Sara
Sedlazeck, Fritz J.
Lippman, Zachary B.
Schatz, Michael C.
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
title RaGOO: fast and accurate reference-guided scaffolding of draft genomes
title_full RaGOO: fast and accurate reference-guided scaffolding of draft genomes
title_fullStr RaGOO: fast and accurate reference-guided scaffolding of draft genomes
title_full_unstemmed RaGOO: fast and accurate reference-guided scaffolding of draft genomes
title_short RaGOO: fast and accurate reference-guided scaffolding of draft genomes
title_sort ragoo: fast and accurate reference-guided scaffolding of draft genomes
topic Method
url 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
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