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KMC 3: counting and manipulating k-mer statistics
Open accessAbstract
Summary: Counting all k-mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k-mer databases. Usefulness of the tools is shown on a few real problems. Availability and implementation: Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc. Supplementary information: Supplementary data are available at Bioinformatics online.
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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
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811 · cited 1×
“/dsk -file fv.fastq -kmer-size 28 -max-memory 12000 -verbose”
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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
Complete genomic and epigenetic maps of human centromeres
Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., et al. (2022) · Science · doi:10.1126/science.abl4178 · Cited by 618
Z-nucleic-acid sensing triggers ZBP1-dependent necroptosis and inflammation
Jiao, H., Wachsmuth, L., Kumari, S., Schwarzer, R., Lin, J., Eren, R. O., Fisher, A., Lane, R., Young, G. R., Kassiotis, G., et al. (2020) · Nature · doi:10.1038/s41586-020-2129-8 · Cited by 486
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411
Genotyping structural variants in pangenome graphs using the vg toolkit
Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020) · Genome Biology · doi:10.1186/s13059-020-1941-7 · Cited by 319
Metadata
- Authors
- Kokot, M., Długosz, M., & Deorowicz, S.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-05-04
- Volume
- 33
- Issue
- 17
- Pages
- 2759-2761
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2583363792
- Cited by
- 750
- References
- 2
- FWCI
- 16.07
- Type
- journal article
- Language
- en
- Open access
- bronze
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