The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
GenomeScope: fast reference-free genome profiling from short reads
Open accessAbstract
Summary: GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates. Availability and Implementation: http://genomescope.org, https://github.com/schatzlab/genomescope.git. Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
Marçais, G., & Kingsford, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr011 · Cited by 4,661
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., et al. (2014) · Genome Research · doi:10.1101/gr.170720.113 · Cited by 1,017
Cited by
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C. (2020) · Nature Communications · doi:10.1038/s41467-020-14998-3 · Cited by 2,759
Self-citationPérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
Metadata
- Authors
- Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., & Schatz, M. C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-03-24
- Volume
- 33
- Issue
- 14
- Pages
- 2202-2204
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2949086752
- Cited by
- 1,839
- References
- 4
- FWCI
- 31.83
- Type
- journal article
- Language
- en
- Open access
- green
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- Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., & Schatz, M. C. (2017). GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx153
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