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KMC specifications

Information


Unique identifier OMICS_02095
Name KMC
Alternative name K-Mer Counter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Sebastian Deorowicz

Publications for K-Mer Counter

KMC citations

 (8)
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

[…] lers, 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 sampled k-mers is importan […]

library_books

Designing small universal k mer hitting sets for improved analysis of high throughput sequencing

2017
PLoS Comput Biol
PMCID: 5645146
PMID: 28968408
DOI: 10.1371/journal.pcbi.1005777

[…] see the benefit of our compact UHSs in many data structures and algorithms that analyze high-throughput sequencing data. For example, we expect that binning-based k-mer counting applications, such as KMC 2 [], can reduce the number of bins, and thus the number of disk accesses, using universal k-mer hitting sets. Analyses that rely on k-mer counting, such as metagenomic binning as implemented in K […]

library_books

Phenetic Comparison of Prokaryotic Genomes Using k mers

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

[…] t 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 more efficie […]

library_books

ntCard: a streaming algorithm for cardinality estimation in genomics data

2017
Bioinformatics
PMCID: 5408799
PMID: 28453674
DOI: 10.1093/bioinformatics/btw832

[…] t detection (), SNP detection (; ) and RNA-seq quantification analysis (). The problem of counting k-mers has been well studied in the literature, including the Jellyfish (), BFCounter (), DSK () and KMC () algorithms. These tools need considerable computational resources and can be improved in terms of memory, disk space and runtime requirements for processing and obtaining the histogram of k-mer […]

library_books

GenomeTester4: a toolkit for performing basic set operations union, intersection and complement on k mer lists

2015
GigaScience
PMCID: 4669650
PMID: 26640690
DOI: 10.1186/s13742-015-0097-y

[…] ctures that facilitate optimal counting for specific cases. For example, Tallymer [] uses a suffix array and specializes in counting k-mers from large eukaryotic genomes with many repeated sequences. KMC2 [] and DSK [] can run on computers with limited memory by writing k-mers into several small temporary tables that are combined onto disk storage. Turtle [] uses a combination of Bloom filter and […]

library_books

Draft Genome Sequence of a European Isolate of the Apple Canker Pathogen Neonectria ditissima

2015
Genome Announc
PMCID: 4653771
PMID: 26586869
DOI: 10.1128/genomeA.01243-15

[…] 389,629 paired-end reads.Adaptor sequences and low-quality data were removed using fastqc-mcf. The sequencing depth was estimated to be 42× and genome size to be 48 Mb, following k-mer counting using KMC (). De novo assembly was performed using SPAdes version 3.1.0 and analyzed using Quast (). The genome was assembled into 45.72 Mb in 675 contigs (>500 bp and >10× coverage), with an N50 metric of […]

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KMC institution(s)
Institute of Informatics, Silesian University of Technology, Gliwice, Poland

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