MSPKmerCounter specifications


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
Maintained No




No version available


This tool is not available anymore.

MSPKmerCounter citations


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

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

[…] disk 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 of samp […]


Phenetic Comparison of Prokaryotic Genomes Using k mers

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 while being general […]

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

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