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DSK specifications

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Unique identifier OMICS_02094
Name DSK
Alternative name Disk Streaming of K-mers
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Disk Streaming of K-mers

DSK in publications

 (5)
PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] a feature vector consists of elements that account for the number of occurrences (i.e., frequency) for each k-mer through all the reads in one metagenomic sample. existing tools, such as dsk () or jellyfish (), are available for counting k-mer frequency. in our study, we used dsk to count k-mers. the reverse complements of reads were taken into consideration. a k-mer and its reverse […]

PMCID: 5850840
PMID: 28957508
DOI: 10.1093/molbev/msx200

[…] interest for quite a while now (; ; ). it is the gold standard for short read assemblies with de bruijn graphs (; ) and there are several highly efficient k-mer counters, like mspkmercounter (), dsk (), and kmc2 (). alignment-free sequence comparisons have been studied in numerous ways and are competitive with alignment-based methods in terms of accuracy while being generally computationally […]

PMCID: 5124939
PMID: 27892531
DOI: 10.1038/srep37811

[…] to reduce the computational time and to mainly understand the topology of the phylogenetic tree., for each strain, we listed all of the unique 31-bp dna motifs, or kmers, in its genome, using the dsk software. we then calculated the difference in the frequency of appearance of each kmer in the carbapenem-resistant and -susceptible populations, and extracted kmers with a more than 70% […]

PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] for a certain alternative on that position, this alternative is reserved as one potential correction., bless [] uses a single minimum-sized bloom filter and disk-based k-mer counting algorithm like disk streaming of k-mers (dsk) [] and k-mer counter (kmc) [] to achieve high memory efficiency for error correction, sequence repeat handling, and read end correction by read extension. briefly, […]

PMCID: 3974045
PMID: 24565280
DOI: 10.1186/1748-7188-9-2

[…] membership queries, this allows us to precisely evaluate our method against the one of []., the first step of the implementation is to retrieve the list of k-mers that appear more than d times using dsk [] – a constant memory streaming algorithm to count k-mers. note, as a side remark, that performing counting allows us to perform off-line deletions of k-mers. that is, if at some point […]


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DSK institution(s)
Algorizk, Paris; ENS Cachan Brittany/IRISA, Rennes, France
DSK funding source(s)
ANR MAPPI; ANR-10-COSI-0004

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