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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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: | bioinformatics > genomics and proteomics > alignment organism description > plant > Arabidopsis bioinformatics bioinformatics > genomics and proteomics Investigative techniques and equipment bioinformatics > genomics and proteomics > alignment > sequence alignment Investigative techniques and equipment > assays Investigative techniques and equipment > assays > long-read sequencing organism description > plant 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: | 01 Feb 2024 20:06 |
| PMCID: | PMC6816165 |
| Related URLs: | |
| Dataset ID: |
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| URI: | https://repository.cshl.edu/id/eprint/38669 |
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