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Supported Applications

KMC

  • Description

    KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. K-mer counting is important for many bioinformatics applications, e.g., developing de Bruijn graph assemblers. Building de Bruijn graphs is a commonly used approach for genome assembly with data from second-generation sequencer. Unfortunately, sequencing errors (frequent in practice) results in huge memory requirements for de Bruijn graphs, as well as long build time. One of the popular approaches to handle this problem is filtering the input reads in such a way that unique k-mers (very likely obtained as a result of an error) are discarded.

  • Usage

    To list all executables provided by KMC, run: $ biogrids-list kmc Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install kmc Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    M. Kokot, M. Dlugosz, and D. S.. 2017. KMC 3: counting and manipulating k-mer statistics. Bioinformatics. 33(17): 2759-2761.


    • *Full citation information available through

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