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PMID: 31661016 Published · epublish English Evaluation Study Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

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

Genome biology ·Vol. 20 ·No. 1 ·2019-00-28 ·Pages 224

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC

Abstract

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 .

Keywords
Genome alignment Genome assembly Long-read sequencing Pseudomolecule Reference-guided Scaffolding Tomato
MeSH Terms
Arabidopsis/genetics Genome, Plant Genomic Structural Variation Genomics/methods Lycopersicon esculentum/genetics Software
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Alonge Michael
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Soyk Sebastian
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Ramakrishnan Srividya
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Wang Xingang
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Goodwin Sara
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Sedlazeck Fritz J
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Lippman Zachary B
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. | Cold Spring Harbor Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY, USA.
Schatz Michael C ORCID
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. [email protected]. | Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. [email protected]. | Department of Biology, Johns Hopkins University, Baltimore, MD, USA. [email protected].
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/s13059-019-1829-6
Email
[email protected]
Published
2019-00-28
Epub
2019-00-28
Pages
224
Language
English
Region
England
NLM ID
100960660
PMCID
PMC6816165
Subset
IM
Grants
NIH HHS · R01-HG006677 · United States
NIH HHS · UM1 HG008898 · United States
External Links
PubMed source DOI: 10.1186/s13059-019-1829-6 PMC Full Text View journal details
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