The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
The khmer software package: enabling efficient nucleotide sequence analysis
Open accessAbstract
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/ .
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Cites
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,987
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,491
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., et al. (2013) · Nature Protocols · doi:10.1038/nprot.2013.084 · Cited by 8,464
HyperLogLog: the analysis of a near-optimal cardinality estimation algorithm
Flajolet, P., Fusy, É., Gandouet, O., & Meunier, F. (2007) · Discrete Mathematics & Theoretical Computer Science · doi:10.46298/dmtcs.3545 · Cited by 695
SeqAn An efficient, generic C++ library for sequence analysis
Döring, A., Weese, D., Rausch, T., & Reinert, K. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-11 · Cited by 333
Tackling soil diversity with the assembly of large, complex metagenomes
Howe, A. C., Jansson, J. K., Malfatti, S. A., Tringe, S. G., Tiedje, J. M., & Brown, C. T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402564111 · Cited by 321
Self-citationIDBA – A Practical Iterative de Bruijn Graph De Novo Assembler
Peng, Y., Leung, H. C. M., Yiu, S. M., & Chin, F. Y. L. (2010) · Lecture Notes in Computer Science · doi:10.1007/978-3-642-12683-3_28 · Cited by 293
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
Pell, J., Hintze, A., Canino-Koning, R., Howe, A., Tiedje, J. M., & Brown, C. T. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121464109 · Cited by 247
Self-citationA Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data
Brown, C. T., Howe, A., Zhang, Q., Pyrkosz, A. B., & Brom, T. H. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1203.4802 · Cited by 228
Self-citationZhang, Q., Pell, J., Canino-Koning, R., Howe, A. C., & Brown, C. T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0101271 · Cited by 109
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Roux, S., Emerson, J. B., Eloe-Fadrosh, E. A., & Sullivan, M. B. (2017) · PeerJ · doi:10.7717/peerj.3817 · Cited by 319
Colbert, L. E., El Alam, M. B., Wang, R., Karpinets, T., Lo, D., Lynn, E. J., Harris, T. A., Elnaggar, J. H., Yoshida-Court, K., Tomasic, K., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.09.012 · Cited by 270
Self-citationGut microorganisms act together to exacerbate inflammation in spinal cords
Miyauchi, E., Kim, S.-W., Suda, W., Kawasumi, M., Onawa, S., Taguchi-Atarashi, N., Morita, H., Taylor, T. D., Hattori, M., & Ohno, H. (2020) · Nature · doi:10.1038/s41586-020-2634-9 · Cited by 268
Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240
Metadata
- Authors
- Crusoe, M. R., Alameldin, H. F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A., Constantinides, B., Edvenson, G., Fay, S., Fenton, J., Fenzl, T., Fish, J., Garcia-Gutierrez, L., Garland, P., Gluck, J., González, I., Guermond, S., Guo, J., Gupta, A., Herr, J. R., Howe, A., Hyer, A., Härpfer, A., Irber, L., Kidd, R., Lin, D., Lippi, J., Mansour, T., McA'Nulty, P., McDonald, E., Mizzi, J., Murray, K. D., Nahum, J. R., Nanlohy, K., Nederbragt, A. J., Ortiz-Zuazaga, H., Ory, J., Pell, J., Pepe-Ranney, C., Russ, Z. N., Schwarz, E., Scott, C., Seaman, J., Sievert, S., Simpson, J., Skennerton, C. T., Spencer, J., Srinivasan, R., Standage, D., Stapleton, J. A., Steinman, S. R., Stein, J., Taylor, B., Trimble, W., Wiencko, H. L., Wright, M., Wyss, B., Zhang, Q., zyme, E., & Brown, C. T.
- Venue
- F1000Research
- Publisher
- F1000 Research Ltd
- Published
- 2015-09-25
- Volume
- 4
- Pages
- 900
- ISSN
- 2046-1402 (ISSN-L)
- OpenAlex
- W1954100204
- Cited by
- 388
- References
- 12
- FWCI
- 16.08
- Type
- journal article
- Language
- en
- Open access
- gold
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- Crusoe, M. R., Alameldin, H. F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A., Constantinides, B., Edvenson, G., Fay, S., Fenton, J., Fenzl, T., Fish, J., Garcia-Gutierrez, L., Garland, P., Gluck, J., González, I., Guermond, S., Guo, J., . . . Brown, C. T. (2015). The khmer software package: enabling efficient nucleotide sequence analysis. F1000Research. https://doi.org/10.12688/f1000research.6924.1
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
