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MSPKmerCounter specifications

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Unique identifier OMICS_07240
Name MSPKmerCounter
Alternative name MSPCounter
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Version 0.10.0
Stability Stable
Source code URL http://www.cs.ucsb.edu/~yangli/MSPKmerCounter/package/MSPKmerCounter-0.10.0-src.zip
Maintained No

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MSPKmerCounter citations

 (3)
library_books

Comparing fixed sampling with minimizer sampling when using k mer indexes to find maximal exact matches

2018
PLoS One
PMCID: 5794061
PMID: 29389989
DOI: 10.1371/journal.pone.0189960

[…] based dbg assemblers, minimizer sampling is used to select m-mers (m < k) from every k-mer. these m-mers are later used to reduce disk i/o operations in disk based counting k-mers tools such as mspkmercounter [] and kmc2 []. again, this problem is significantly different than our motivating problems which are searching for mems and hslas. in mem and hsla search problems, the location […]

library_books

Phenetic Comparison of Prokaryotic Genomes Using k mers

2017
Mol Biol Evol
PMCID: 5850840
PMID: 28957508
DOI: 10.1093/molbev/msx200

[…] attracted researchers’ 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 […]

library_books

Improving the performance of minimizers and winnowing schemes

2017
Bioinformatics
PMCID: 5870760
PMID: 28881970
DOI: 10.1093/bioinformatics/btx235

[…] we look at the potential effect of using universal hitting set orderings on bioinformatics applications. in the case of dna sequence binning, such as performed by the k-mer counters kmc2 () and mspkmercounter (), we compare the distribution of the number and sizes of bins created by different orderings proposed in the literature. the universal hitting sets ordering perform better […]


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MSPKmerCounter institution(s)
University of California, Santa Barbara, CA, USA

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