The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Informed and automated k-mer size selection for genome assembly
Abstract
Motivation: Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically estimate the best k to use and/or quickly generate histograms of k-mer abundances that would allow the user to make an informed decision. Results: We develop a fast and accurate sampling method that constructs approximate abundance histograms with several orders of magnitude performance improvement over traditional methods. We then present a fast heuristic that uses the generated abundance histograms for putative k values to estimate the best possible value of k. We test the effectiveness of our tool using diverse sequencing datasets and find that its choice of k leads to some of the best assemblies. Availability: Our tool KmerGenie is freely available at: http://kmergenie.bx.psu.edu/. Contact: pashadag@cse.psu.edu
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Citations
Cites
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
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
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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
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.023 · Cited by 619
Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction
Laehnemann, D., Borkhardt, A., & McHardy, A. C. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbv029 · Cited by 296
Metadata
- Authors
- Chikhi, R., & Medvedev, P.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-06-03
- Volume
- 30
- Issue
- 1
- Pages
- 31-37
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2104677379
- Cited by
- 721
- References
- 2
- FWCI
- 15.20
- Type
- journal article
- Language
- en
- Open access
- closed
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