The DOI matches its Crossref record; 67 of the 67 references it cites were found in a registry or an index.
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Open accessAbstract
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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Cites
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The Sequence Alignment/Map format and SAMtools
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
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Cited by
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
Goel, M., Sun, H., Jiao, W.-B., & Schneeberger, K. (2019) · Genome Biology · doi:10.1186/s13059-019-1911-0 · Cited by 1,045
Alonge, M., Lebeigle, L., Kirsche, M., Jenike, K., Ou, S., Aganezov, S., Wang, X., Lippman, Z. B., Schatz, M. C., & Soyk, S. (2022) · Genome Biology · doi:10.1186/s13059-022-02823-7 · Cited by 992
Self-citationMajor Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.021 · Cited by 819
Self-citationThe genetic and epigenetic landscape of the Arabidopsis centromeres
Naish, M., Alonge, M., Wlodzimierz, P., Tock, A. J., Abramson, B. W., Schmücker, A., Mandáková, T., Jamge, B., Lambing, C., Kuo, P., et al. (2021) · Science · doi:10.1126/science.abi7489 · Cited by 458
Self-citationPan-genomics in the human genome era
Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 359
Metadata
- Authors
- Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., & Schatz, M. C.
- Venue
- Genome Biology
- Published
- 2019-10-28
- Volume
- 20
- Issue
- 1
- Pages
- 224-224
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2981615389
- Cited by
- 685
- References
- 67
- FWCI
- 25.85
- Type
- journal article
- Language
- en
- Open access
- gold
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- Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., & Schatz, M. C. (2019). RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biology. https://doi.org/10.1186/s13059-019-1829-6
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