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

Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., Schatz, M. C. (October 2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20 (1). p. 224. ISSN 1474-7596 (Public Dataset)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/31661016
DOI: 10.1186/s13059-019-1829-6

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 .

Item Type: Paper
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > alignment > sequence alignment
Investigative techniques and equipment > assays > long-read sequencing
organism description > plant > tomato
CSHL Authors:
Communities: CSHL labs > Lippman lab
CSHL labs > Schatz lab
Depositing User: Matthew Dunn
Date: 28 October 2019
Date Deposited: 08 Nov 2019 15:32
Last Modified: 08 Nov 2019 15:32
PMCID: PMC6816165
Related URLs:
Dataset ID:
  • Code: https://github.com/malonge/RaGOO
URI: https://repository.cshl.edu/id/eprint/38669

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