MSPKmerCounter specifications

Information


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

 (2)
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

[…] 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 […]

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 while being general […]

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

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